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Opened 105 minutes ago
#19800 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-26.1-arm64-arm-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Current thread 0x00000001f93f2080 (most recent call first):
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/windowsize.py", line 49 in window_size
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3221 in run
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1057 in init
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 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.map._map, openmm._openmm, openmm.app.internal.xtc_utils, openmm.app.internal.compiled, chimerax.pdb_lib._load_libs, psutil._psutil_osx, psutil._psutil_posix, chimerax.surface._surface, 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, PIL._imaging, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree (total: 58)
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{
"uptime" : 110000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac15,9",
"coalitionID" : 11292,
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"build" : "25B78",
"releaseType" : "User"
},
"captureTime" : "2026-02-03 19:48:57.4720 +0100",
"codeSigningMonitor" : 2,
"incident" : "5DAD8176-7415-4310-813E-6F24C847C361",
"pid" : 47468,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2026-02-03 19:47:56.1640 +0100",
"procStartAbsTime" : 2663808204118,
"procExitAbsTime" : 2665279422175,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.10.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.10.1","CFBundleVersion":"1.10.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"006E10D4-D1DB-52B2-84F3-C612941A6EDE","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "274B254F-743F-07AD-6EDC-065EDC9CDAF2",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["selectedLanguageDoesNotMatchSelectedSiriLanguageInfo(system: en, siri: en-GB)","selectedLanguageDoesNotMatchSelectedSiriLanguage"]},
"developerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRFOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkQng\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "6FA3E6D8-B5BF-4900-919B-2A35D149ABE3",
"wakeTime" : 704,
"sleepWakeUUID" : "449FDA8F-5365-4D8F-934D-A49997EDDFB3",
"sip" : "enabled",
"exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
"termination" : {"flags":0,"code":6,"namespace":"SIGNAL","indicator":"Abort trap: 6","byProc":"ChimeraX","byPid":47468},
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"faultingThread" : 0,
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===== Log before crash start =====
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/lorenz.grundmann/VBC Dropbox/Group Folder
> Haselbach/Projects/HERC1/Lorenz/ChimeraX_session/PSCM5-PAAF1-Herc1/20260203_interactions.cxs"
Opened 20260203_frankemnmap.mrc as #2, grid size 360,360,360, pixel 1.27,
shown at level 0.0765, step 1, values float32
Opened cryosparc_P615_J1927_014_volume_map.mrc as #5, grid size 360,360,360,
pixel 1.27, shown at level 0.229, step 1, values float32
Opened 20260203_frankemnmap.mrc copy as #7, grid size 360,360,360, pixel 1.27,
shown at level 0.0765, step 1, values float32
Log from Tue Feb 3 16:26:41 2026UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/lorenz.grundmann/VBC Dropbox/Group Folder
> Haselbach/Projects/HERC1/Lorenz/P615_ZH027_ZH034-xlinked_P5P1_occupancy/analysis.cxs"
Opened cryosparc_P615_J1783_volume_map.mrc as #8, grid size 360,360,360, pixel
1.27, shown at level 0.0846, step 1, values float32
Opened cryosparc_P615_J1786_volume_map.mrc as #9, grid size 360,360,360, pixel
1.27, shown at level 0.0846, step 1, values float32
Opened cryosparc_P615_J1843_volume_map.mrc as #10, grid size 360,360,360,
pixel 1.27, shown at level 0.0846, step 1, values float32
Opened cryosparc_P615_J1846_volume_map.mrc as #11, grid size 360,360,360,
pixel 1.27, shown at level 0.0846, step 1, values float32
Opened cryosparc_P615_J1930_volume_map.mrc as #14, grid size 360,360,360,
pixel 1.27, shown at level 0.09, step 1, values float32
Opened cryosparc_P615_J1932_volume_map.mrc as #15, grid size 360,360,360,
pixel 1.27, shown at level 0.09, step 1, values float32
Opened cryosparc_P615_J1934_volume_map.mrc as #16, grid size 360,360,360,
pixel 1.27, shown at level 0.09, step 1, values float32
Opened cryosparc_P615_J1936_volume_map.mrc as #19, grid size 360,360,360,
pixel 1.27, shown at level 0.09, step 1, values float32
Opened cryosparc_P615_J772_011_volume_map.mrc as #1, grid size 360,360,360,
pixel 1.27, shown at level 0.099, step 1, values float32
Opened cryosparc_P615_J528_mask.mrc as #2, grid size 240,240,240, pixel 1.9,
shown at level 0.5, step 1, values float32
Opened cryosparc_P615_J526_mask (1).mrc as #3, grid size 240,240,240, pixel
1.9, shown at level 0.5, step 1, values float32
Opened cryosparc_P615_J453_mask (1).mrc as #4, grid size 360,360,360, pixel
1.27, shown at level 0.5, step 2, values float32
Opened cryosparc_P615_J1711_volume_map.mrc as #5, grid size 360,360,360, pixel
1.27, shown at level 0.083, step 1, values float32
Opened cryosparc_P615_J1714_volume_map.mrc as #6, grid size 360,360,360, pixel
1.27, shown at level 0.099, step 1, values float32
Log from Mon Jan 19 11:45:42 2026 Startup Messages
---
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr bundle with that from OME-Zarr bundle
Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Volumes/Herc/20241024_ZH027_Hek_Herc1_PSMC5_PAAF1/relion/J448/Refine3D/lp-12/run_class001.mrc
Opened run_class001.mrc as #1, grid size 360,360,360, pixel 1.27, shown at
level 0.00123, step 2, values float32
> volume #1 level 0.00391
> volume #1 step 1
> volume #1 level 0.004416
> open
> /Users/lorenz.grundmann/Downloads/cryosparc_P713_J541_002_volume_map.mrc
Opened cryosparc_P713_J541_002_volume_map.mrc as #2, grid size 256,256,256,
pixel 0.951, shown at level 0.0567, step 1, values float32
> hide #!1 models
> view #2 clip false
> volume #2 level 0.1409
> open
> /Users/lorenz.grundmann/Downloads/fold_herc1_zinc/fold_herc1_zinc_model_0.cif
Summary of feedback from opening
/Users/lorenz.grundmann/Downloads/fold_herc1_zinc/fold_herc1_zinc_model_0.cif
---
note | Fetching CCD ZN from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif
Chain information for fold_herc1_zinc_model_0.cif #3
---
Chain | Description
A | .
> hide #!2 models
> select /A:372-739
2719 atoms, 2772 bonds, 368 residues, 1 model selected
> show sequence sel
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 3/A
No active region
> select /A:739
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:420-739
2348 atoms, 2392 bonds, 320 residues, 1 model selected
> select /A:372-739
2719 atoms, 2772 bonds, 368 residues, 1 model selected
> select /A:1987-2027
336 atoms, 339 bonds, 41 residues, 1 model selected
> select /A:2027-2358
2603 atoms, 2653 bonds, 332 residues, 1 model selected
> select /A:2027-2193
1304 atoms, 1335 bonds, 167 residues, 1 model selected
> open
> /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/relion/J772_preP5P1-class_consensus_C3-relaxed/Class3D/dimer_2_iAlign_cl3_blush/run_it025_class001.mrc
Opened run_it025_class001.mrc as #4, grid size 360,360,360, pixel 1.27, shown
at level 2.54e-06, step 2, values float32
> open
> /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/relion/J772_preP5P1-class_consensus_C3-relaxed/Class3D/dimer_2_iAlign_cl3_blush/run_it025_class002.mrc
Opened run_it025_class002.mrc as #5, grid size 360,360,360, pixel 1.27, shown
at level 2.38e-06, step 2, values float32
> open
> /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/relion/J772_preP5P1-class_consensus_C3-relaxed/Class3D/dimer_2_iAlign_cl3_blush/run_it025_class003.mrc
Opened run_it025_class003.mrc as #6, grid size 360,360,360, pixel 1.27, shown
at level 8.79e-07, step 2, values float32
> hide #3 models
> view #5 clip false
> volume #4 level 0.006078
> volume #5 level 0.005325
> volume #6 level 0.004012
> open
> /Volumes/Herc/20230421_Herc_WT/model_building/model_finalisation/RLD1_PCNA/phenix/RealSpaceRefine_2/20250108_RLDs-
> fitted_real_space_refined_002.cif
Summary of feedback from opening
/Volumes/Herc/20230421_Herc_WT/model_building/model_finalisation/RLD1_PCNA/phenix/RealSpaceRefine_2/20250108_RLDs-
fitted_real_space_refined_002.cif
---
warnings | Skipping chem_comp category: Missing column 'type' near line 510
Missing entity information. Treating each chain as a separate entity.
Invalid residue range for struct_conf "1": invalid chain "1", near line 138
Invalid residue range for struct_conf "2": invalid chain "1", near line 139
Invalid residue range for struct_conf "3": invalid chain "1", near line 140
Invalid residue range for struct_conf "4": invalid chain "1", near line 141
Invalid residue range for struct_conf "5": invalid chain "1", near line 142
31 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "1 1": invalid chain "1", near line
392
Invalid sheet range for struct_sheet_range "2 1": invalid chain "1", near line
393
Invalid sheet range for struct_sheet_range "3 1": invalid chain "1", near line
394
Invalid sheet range for struct_sheet_range "4 1": invalid chain "1", near line
395
Invalid sheet range for struct_sheet_range "5 1": invalid chain "1", near line
396
112 messages similar to the above omitted
Atom H1 is not in the residue template for VAL /1:512
Atom H1 is not in the residue template for GLY /1:633
Atom H1 is not in the residue template for THR /1:665
Atom H1 is not in the residue template for SER /1:675
Atom H3 is not in the residue template for PRO /1:705
Atom H is not in the residue template for LYS /1:1384
Atom H1 is not in the residue template for VAL /2:512
Atom H1 is not in the residue template for GLY /2:633
Atom H1 is not in the residue template for THR /2:665
Too many hydrogens missing from residue template(s) to warn about
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for 20250108_RLDs-fitted_real_space_refined_002.cif #7
---
Chain | Description
1 2 | No description available
3 | No description available
Ba Bb Bc | No description available
> hide #!6 models
> show sequence #7/1
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> sequence chain #7/1
Alignment identifier is 7/1
> select #7/1:1399
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #7/1
5120 atoms, 5166 bonds, 7 pseudobonds, 344 residues, 2 models selected
> open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1783_volume_map.mrc
Opened cryosparc_P615_J1783_volume_map.mrc as #8, grid size 360,360,360, pixel
1.27, shown at level 0.101, step 2, values float32
> open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1786_volume_map.mrc
Opened cryosparc_P615_J1786_volume_map.mrc as #9, grid size 360,360,360, pixel
1.27, shown at level 0.0998, step 2, values float32
> hide #!7 models
> volume #8 level 0.07925
> volume #9 level 0.08883
> volume #9 step 1
> volume #8 step 1
> volume #9 level 0.09891
> volume #9 level 0.08782
> open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1843_volume_map.mrc
Opened cryosparc_P615_J1843_volume_map.mrc as #10, grid size 360,360,360,
pixel 1.27, shown at level 0.0985, step 2, values float32
> hide #!8 models
> hide #!9 models
> open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1846_volume_map.mrc
Opened cryosparc_P615_J1846_volume_map.mrc as #11, grid size 360,360,360,
pixel 1.27, shown at level 0.103, step 2, values float32
> hide #!10 models
> show #!10 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> volume #11 step 1
> volume #10 step 1
> show #!11 models
> hide #!11 models
> show #!11 models
> volume #10 level 0.07064
> volume #10 level 0.09529
> show #!8 models
> show #!9 models
> hide #!10 models
> show #!10 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!10 models
> hide #!11 models
> volume #9 level 0.09589
> volume #8 level 0.08615
> volume #9 level 0.06767
> volume #10 level 0.0835
> volume #9 level 0.08178
> show #!11 models
> hide #!10 models
> hide #!9 models
> show #!10 models
> volume #10 level 0.08457
> open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1873_volume_map.mrc
Opened cryosparc_P615_J1873_volume_map.mrc as #12, grid size 360,360,360,
pixel 1.27, shown at level 0.099, step 2, values float32
> open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1876_volume_map.mrc
Opened cryosparc_P615_J1876_volume_map.mrc as #13, grid size 360,360,360,
pixel 1.27, shown at level 0.102, step 2, values float32
> volume #12 step 1
> volume #13 step 1
> volume #13 level 0.1007
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> show #!8 models
> hide #!9 models
> hide #!8 models
> show #!10 models
> hide #!10 models
> show #!9 models
> show #!8 models
> hide #!12 models
> hide #!13 models
> hide #!8 models
> hide #!9 models
> show #!10 models
> show #!11 models
> show #!13 models
> hide #!13 models
> show #!12 models
> hide #!11 models
> show #!9 models
> hide #!10 models
> hide #!9 models
> show #!13 models
> show #!10 models
> show #!11 models
> hide #!12 models
> hide #!13 models
> hide #!10 models
> hide #!11 models
> show #!9 models
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> volume #9 level 0.09286
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> show #!8 models
> show #!10 models
> hide #!9 models
> hide #!8 models
> show #!11 models
> hide #!10 models
> hide #!11 models
> show #!8 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> show #!9 models
> hide #!8 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> show #!8 models
> hide #!9 models
> show #!11 models
> hide #!10 models
> show #!10 models
> hide #!11 models
> show #!13 models
> hide #!10 models
> hide #!8 models
> show #!10 models
> close #12-13
> show #!9 models
> volume #9 level 0.09488
> show #!8 models
> volume #8 level 0.07039
> hide #!9 models
> hide #!10 models
> show #!11 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> show #!7 models
> hide #!7 models
> show #!9 models
> hide #!11 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1873_volume_map.mrc
Opened cryosparc_P615_J1873_volume_map.mrc as #12, grid size 360,360,360,
pixel 1.27, shown at level 0.099, step 2, values float32
> hide #!9 models
> open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1876_volume_map.mrc
Opened cryosparc_P615_J1876_volume_map.mrc as #13, grid size 360,360,360,
pixel 1.27, shown at level 0.102, step 2, values float32
> volume #12 level 0.06835
> volume #12 level 0.0958
> volume #13 level 0.09404
> open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1930_volume_map.mrc
Opened cryosparc_P615_J1930_volume_map.mrc as #14, grid size 360,360,360,
pixel 1.27, shown at level 0.105, step 2, values float32
> hide #!12 models
> hide #!13 models
> volume #14 level 0.08558
> volume #14 step 1
> open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1932_volume_map.mrc
Opened cryosparc_P615_J1932_volume_map.mrc as #15, grid size 360,360,360,
pixel 1.27, shown at level 0.0999, step 2, values float32
> hide #!14 models
> volume #15 level 0.07598
> open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1934_volume_map.mrc
Opened cryosparc_P615_J1934_volume_map.mrc as #16, grid size 360,360,360,
pixel 1.27, shown at level 0.0991, step 2, values float32
> hide #!15 models
> volume #16 level 0.08652
> show #!15 models
> show #!14 models
> show #!13 models
> hide #!14 models
> hide #!15 models
> hide #!16 models
> show #!14 models
> hide #!13 models
> set bgColor white
> hide #!14 models
> color #14-16 darkgrey
> show #!14 models
> show #!15 models
> show #!16 models
> hide #!15 models
> hide #!14 models
> open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
> model/20250505_P5P1-SPRY-RLD1_isolde_clean.pdb
Chain information for 20250505_P5P1-SPRY-RLD1_isolde_clean.pdb #17
---
Chain | Description
1 | No description available
A | No description available
B | No description available
> hide #!16 models
> show #!16 models
> open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
> model/20250902_composite_chain-fix.pdb
Chain information for 20250902_composite_chain-fix.pdb #18
---
Chain | Description
1 2 3 | No description available
A I K | No description available
B J L | No description available
> hide #!16 models
> show #17#!18 cartoons
> hide #17#!18 atoms
> show #!14 models
> show #!15 models
> hide #!15 models
> hide #!14 models
> show #!15 models
> show #!16 models
> hide #!15 models
> hide #!16 models
> select #18/1:3783
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
98 atoms, 97 bonds, 6 residues, 1 model selected
> select up
7957 atoms, 8046 bonds, 538 residues, 1 model selected
> select up
8105 atoms, 8193 bonds, 547 residues, 1 model selected
> select up
10637 atoms, 10758 bonds, 717 residues, 1 model selected
> select up
10868 atoms, 10992 bonds, 732 residues, 1 model selected
> select up
14205 atoms, 14374 bonds, 943 residues, 1 model selected
> select up
14286 atoms, 14455 bonds, 948 residues, 1 model selected
> select up
21639 atoms, 21880 bonds, 1408 residues, 1 model selected
> select #18/!
Expected an objects specifier or a keyword
> select #18/1
54175 atoms, 54698 bonds, 35 pseudobonds, 3516 residues, 2 models selected
> intersect dimer 1, 2 occpued, dimer 3 empty
Unknown command: intersect dimer 1, 2 occpued, dimer 3 empty
> color sel #d31340ff
> show #!16 models
> color sel #b2b2b2
> color sel #F6921E
> select up
193662 atoms, 195518 bonds, 105 pseudobonds, 12558 residues, 2 models selected
> select up
193662 atoms, 195518 bonds, 105 pseudobonds, 12558 residues, 2 models selected
> select #18/1:3561
19 atoms, 18 bonds, 1 residue, 1 model selected
> solor #18/1 #663399
Unknown command: solor #18/1 #663399
> color #18/1 #663399
> select /A:2027-2193
1304 atoms, 1335 bonds, 167 residues, 1 model selected
> select #18/1
54175 atoms, 54698 bonds, 35 pseudobonds, 3516 residues, 2 models selected
> color sel #b2b2b2
> select #18/3
54175 atoms, 54694 bonds, 35 pseudobonds, 3516 residues, 2 models selected
> color sel #6120AC
> select #18/2:3560
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #18/2
54175 atoms, 54709 bonds, 35 pseudobonds, 3516 residues, 2 models selected
> color sel #C691FF
> hide #!16 models
> hide #17 models
> select #18/A,B
10283 atoms, 10366 bonds, 669 residues, 1 model selected
> color sel #abd9e533
> color sel #abd9e533 transparency 0
> select #18/B
4397 atoms, 4428 bonds, 277 residues, 1 model selected
> color sel cyan
> color sel light blue
> color sel blue
> color sel sky blue
> color sel powder blue
> color sel steel blue
> select #18/l,K
10283 atoms, 10366 bonds, 669 residues, 1 model selected
> color sel #ffb1fd33
> color sel #ffb1fd33 transparency 0
> select #18/L:278
14 atoms, 13 bonds, 1 residue, 1 model selected
> color #18/L orchid
> color #18/I,J sea green
> select #18/1:192
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #18/I:378
11 atoms, 10 bonds, 1 residue, 1 model selected
> color #18/I light green
> select up
93 atoms, 93 bonds, 6 residues, 1 model selected
> select up
5886 atoms, 5938 bonds, 392 residues, 1 model selected
> color #18/1 #b2b2b2 transparency 80
> color #18/2 #C691FF transparency 80
> color #18/3 #6120AC transparency 80
> show #!14 models
> color zone #14 near #18 distance 8
> hide #!18 models
> color #14-16 white transparency 80
> color zone #14 near #18 distance 8
> color #14-16 white transparency 100
> color zone #14 near #18 distance 8
> color zone #14 near #18 distance 10
[Repeated 1 time(s)]
> color zone #14 near #18 distance 12
> color zone #14 near #18 distance 14
> color zone #14 near #18 distance 20
> show #!18 models
> hide #!14 models
> show sel atoms
> hide sel atoms
[Repeated 1 time(s)]
> show #18
> select #18/A,B,C
10379 atoms, 10461 bonds, 670 residues, 1 model selected
> select #18/A,H,D
6078 atoms, 6128 bonds, 394 residues, 1 model selected
> delete sel]
Missing or invalid "atoms" argument: only initial part "sel" of atom specifier
valid
> delete sel
> undo
Undo failed, probably because structures have been modified.
> close #18
> open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
> model/20250902_composite_chain-fix.pdb
Chain information for 20250902_composite_chain-fix.pdb #18
---
Chain | Description
1 2 3 | No description available
A I K | No description available
B J L | No description available
> color #18/1 #663399
> select /A:2027-2193
1304 atoms, 1335 bonds, 167 residues, 1 model selected
> select #18/1
54175 atoms, 54698 bonds, 35 pseudobonds, 3516 residues, 2 models selected
> color sel #b2b2b2
> select #18/3
54175 atoms, 54694 bonds, 35 pseudobonds, 3516 residues, 2 models selected
> color sel #6120AC
> select #18/2
54175 atoms, 54709 bonds, 35 pseudobonds, 3516 residues, 2 models selected
> color sel #C691FF
> select #18/A,B
10283 atoms, 10366 bonds, 669 residues, 1 model selected
> color sel #abd9e533
> color sel #abd9e533 transparency 0
> select #18/B
4397 atoms, 4428 bonds, 277 residues, 1 model selected
> color sel cyan
> color sel light blue
> color sel blue
> color sel sky blue
> color sel powder blue
> color sel steel blue
> select #18/l,K
10283 atoms, 10366 bonds, 669 residues, 1 model selected
> color sel #ffb1fd33
> color sel #ffb1fd33 transparency 0
> color #18/L orchid
> color #18/I,J sea green
> color #18/I light green
> color #18/1 #b2b2b2 transparency 80
> color #18/2 #C691FF transparency 80
> color #18/3 #6120AC transparency 80
> select #18/C,D,H
288 atoms, 285 bonds, 3 residues, 1 model selected
> delete sel
> show #!14 models
> show #!15 models
> hide #!14 models
> hide #!15 models
> show #!14 models
> hide #!14 models
> show #!15 models
> hide #!18 models
> show #!18 models
> color #14-16 white transparecny 80
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #14-16 white transparency 80
> color #14-16 white transparency 100
> color #14-16 white transparency 80
> show #!14 models
> hide #!15 models
> color zone #14 near #18 distance 20
> hide #!18 models
> show #!15 models
> hide #!14 models
> show #!18 models
> color zone #14 near #18 & ~/I,J distance 20
> color zone #14 near #18 distance 20
> color zone #15 near #18 & ~/I,J distance 20
> show #!16 models
> hide #!15 models
> color zone #15 near #18 & ~/K,L distance 20
> color #14-16 white transparency 80
> color zone #14 near #18 distance 20
> color zone #15 near #18 & ~/I,J distance 20
> color zone #16 near #18 & ~/K,L distance 20
> hide #!18 models
> color #16 white transparency 80
> color zone #16 near #18 & ~/I,J,K,L distance 20
> show #!15 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!15 models
> hide #!16 models
> hide #!14 models
> show #!14 models
> open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1936_volume_map.mrc
Opened cryosparc_P615_J1936_volume_map.mrc as #19, grid size 360,360,360,
pixel 1.27, shown at level 0.104, step 2, values float32
> hide #!14 models
> show #!14 models
> volume #19 step 1
> volume #16 step 1
> volume #15 step 1
> volume #13 step 1
> volume #19 level 0.08332
> hide #!14 models
> show #!18 models
> color zone #19 near #18 & ~/K,L distance 20
> hide #!19 models
> show #!19 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> volume #19 level 0.1091
> volume #19 level 0.0865
> color #19 white transparency 80
> color zone #19 near #18 & ~/K,L distance 20
> color #19 white transparency 100
> color zone #19 near #18 & ~/K,L distance 20
> graphics silhouettes true width 4
> graphics silhouettes true width 2
> volume #19 level 0.1
> volume #16 level 0.1
> show #!16 models
> hide #!19 models
> show #!15 models
> hide #!16 models
> volume #15 level 0.1
> volume #14 level 0.1
> show #!14 models
> hide #!15 models
> volume #14 level 0.09
> show #!15 models
> hide #!14 models
> volume #15 level 0.9
> volume #15 level 0.09
> show #!16 models
> hide #!15 models
> volume #16 level 0.09
> volume #19 level 0.09
> show #!19 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!16 models
> show #!16 models
> hide #!19 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> show #!19 models
> show #!18 models
> hide #!19 models
> hide #!16 models
> hide #!15 models
> show #!18 cartoons
> hide #!18 atoms
> color #18/A ABAA00
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #18/A #ABAA00
> color #18/B #ABAA00
> color #18/A #363600
> color #18/K 005A4A
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #18/K #005A4A
> color #18/L #2CC9A6
> color #18/I #1F2A44
> color #18/J #5B7DBB
> color #14-16,19 white transparency 80
> color zone #19 near #18 & ~/K,L distance 20
> color zone #16 near #18 & ~/I,J,K,L distance 20
> color zone #15 near #18 & ~/I,J distance 20
> color zone #14 near #18 distance 20
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!18 models
> show #!16 models
> hide #!19 models
> show #!15 models
> hide #!16 models
> show #!14 models
> hide #!15 models
> show #!15 models
> hide #!14 models
> show #!16 models
> hide #!15 models
> show #!19 models
> hide #!19 models
> show #!15 models
> hide #!15 models
> hide #!16 models
> show #!14 models
> view name bottom_overview
> close #3#1-2,4-7
> open
> /Users/lorenz.grundmann/Downloads/cryosparc_P615_J772_011_volume_map.mrc
Opened cryosparc_P615_J772_011_volume_map.mrc as #1, grid size 360,360,360,
pixel 1.27, shown at level 0.099, step 2, values float32
> hide #!14 models
> volume #1 step 1
> color #1 darkgrey
> open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J528_mask.mrc
Opened cryosparc_P615_J528_mask.mrc as #2, grid size 240,240,240, pixel 1.9,
shown at level 5e-05, step 1, values float32
> volume #2 level 0.3808
> open "/Users/lorenz.grundmann/Downloads/cryosparc_P615_J526_mask (1).mrc"
Opened cryosparc_P615_J526_mask (1).mrc as #3, grid size 240,240,240, pixel
1.9, shown at level 5e-05, step 1, values float32
> open "/Users/lorenz.grundmann/Downloads/cryosparc_P615_J453_mask (1).mrc"
Opened cryosparc_P615_J453_mask (1).mrc as #4, grid size 360,360,360, pixel
1.27, shown at level 5e-05, step 2, values float32
> hide #!2 models
> hide #!3 models
> hide #!4 models
> show #!18 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> show #!1 models
> hide #!4 models
> show #!16 models
> hide #!16 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> volume #2 level 0.5
> volume #3 level 0.5
> volume #4 level 0.5
> color #4 #707000 transparency 80
> show #!2 models
> hide #!4 models
> color #2 #168E78 transparency 80
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!2 models
> color #3 #168E78 transparency 80
> color #2 #3D5480 transparency 80
> show #!2 models
> show #!4 models
> hide #!18 models
> show #!1 models
> view name side_overview
> turn x 90
[Repeated 3 time(s)]
> turn x -90
> turn z -45
> turn z -120
[Repeated 2 time(s)]
> turn z 120
> view name bottom_overview
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> cd "/Users/lorenz.grundmann/VBC Dropbox/Group Folder
> Haselbach/Projects/HERC1/Lorenz/P615_ZH027_ZH034-xlinked_P5P1_occupancy"
Current working directory is: /Users/lorenz.grundmann/VBC Dropbox/Group Folder
Haselbach/Projects/HERC1/Lorenz/P615_ZH027_ZH034-xlinked_P5P1_occupancy
> save J772_consensus_bottom.png width 3000 height 3000 supersample 3
> transparentBackground true
> view list
Named views: bottom_overview, side_overview
> view side_overview
> save J772_consensus_side.png width 3000 height 3000 supersample 3
> transparentBackground true
> graphics silhouettes true width 4
> view bottom_overview
> save J772_consensus_bottom.png width 3000 height 3000 supersample 3
> transparentBackground true
> view side_overview
> save J772_consensus_side.png width 3000 height 3000 supersample 3
> transparentBackground true
> lighting full
> lighting soft
> save J772_consensus_side.png width 3000 height 3000 supersample 3
> transparentBackground true
> view bottom_overview
> save J772_consensus_bottom.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> show #!14 models
> show #!2 models
> hide #!2 models
> hide all models
> shoe #14 model
Unknown command: shoe #14 model
> view bottom overview
Expected an objects specifier or a view name or a keyword
> view bottom_overview
> show #14 models
> save J1930_arm-1-2-3_occupied_bottom.png width 3000 height 3000 supersample
> 3 transparentBackground true
> show #!15 models
> hide #!14 models
> show #!14 models
> hide #!15 models
> hide #14 models
> show #15 models
> save J1932_arm-1-2_occupied_bottom.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #15 models
> show #16 models
> save J1934_arm-1_occupied_bottom.png width 3000 height 3000 supersample 3
> transparentBackground true
> show #!19 models
> hide #!19 models
> hide #16 models
> show #19 models
> save J1934_arm-1-3_occupied_bottom.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide all models
> view side_overview
> show #14 models
> save J1930_arm-1-2-3_occupied_side.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #14 models
> show #15 models
> save J1932_arm-1-2_occupied_side.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #15 models
> show #16 models
> save J1934_arm-1_occupied_side.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #16 models
> show #19 models
> save J1934_arm-1-3_occupied_side.png width 3000 height 3000 supersample 3
> transparentBackground true
> save occupancy_analysis.cxs includeMaps true
> hide #!19 models
> show #!16 models
> hide #!16 models
> show #!19 models
> color #4 #707000 transparency 20
> color #2 #168E78 transparency 20
> color #2 #3D5480 transparency 20
> color #18/3 #6120AC transparency 20
> color #18/1 #b2b2b2 transparency 20
> color #18/2 #C691FF transparency 20
> color #18/A #ABAA00
> color #18/B #ABAA00
> color #18/A #363600
> color #18/K #005A4A
> color #18/L #2CC9A6
> color #18/I #1F2A44
> color #18/J #5B7DBB
> color zone #14 near #18 distance 20
> color #14-16,19 white transparency 20
> color zone #19 near #18 & ~/K,L distance 20
> color zone #16 near #18 & ~/I,J,K,L distance 20
> color zone #15 near #18 & ~/I,J distance 20
> color zone #14 near #18 distance 20
> show #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #1-4 models
> hide #!19 models
> hide all models
> view bottom_overview
> show #1-4 models
> save J772_consensus_bottom.png width 3000 height 3000 supersample 3
> transparentBackground true
> show #14 models
> save J1930_arm-1-2-3_occupied_bottom.png width 3000 height 3000 supersample
> 3 transparentBackground true
> hide #14 models
> show #15 models
> save J1932_arm-1-2_occupied_bottom.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #15 models
> show #16 models
> save J1934_arm-1_occupied_bottom.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #16 models
> show #19 models
> save J1934_arm-1-3_occupied_bottom.png width 3000 height 3000 supersample 3
> transparentBackground true
> Make the figures
Unknown command: Make the figures
> hide all models
> view bottom_overview
> show #1-4 models
> hide all models
> save J772_consensus_bottom.png width 3000 height 3000 supersample 3
> transparentBackground true
> show #14 models
> save J1930_arm-1-2-3_occupied_bottom.png width 3000 height 3000 supersample
> 3 transparentBackground true
> hide #14 models
> show #15 models
> save J1932_arm-1-2_occupied_bottom.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #15 models
> show #16 models
> save J1934_arm-1_occupied_bottom.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #16 models
> show #19 models
> save J1934_arm-1-3_occupied_bottom.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide all models
> view bottom_overview
> show #1-4 models
> save J772_consensus_bottom.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide all models
> color #4 #707000 transparency 50
> color #2 #168E78 transparency 50
> color #2 #3D5480 transparency 50
> hide all models
> view bottom_overview
> show #1-4 models
> save J772_consensus_bottom.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide all models
> show #14 models
> save J1930_arm-1-2-3_occupied_bottom.png width 3000 height 3000 supersample
> 3 transparentBackground true
> hide #14 models
> show #15 models
> save J1932_arm-1-2_occupied_bottom.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #15 models
> show #16 models
> save J1934_arm-1_occupied_bottom.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #16 models
> show #19 models
> save J1934_arm-1-3_occupied_bottom.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide all models
> view side_overview
> show #1-4 models
> save J772_consensus_side.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide all models
> show #14 models
> save J1930_arm-1-2-3_occupied_side.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #14 models
> show #15 models
> save J1932_arm-1-2_occupied_side.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #15 models
> show #16 models
> save J1934_arm-1_occupied_side.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #16 models
> show #19 models
> save J1934_arm-1-3_occupied_side.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #!19 models
> show #!4 models
> hide #!4 models
> show #8 models
> show #8-16 models
> hide #!14-16 target m
> hide #!10-13 target m
> hide #!9 models
> hide #!8 models
> show #!9 models
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> volume #8 level 0.0949
> volume #9 level 0.0846
> volume #8 level 0.0846
> volume #11 level 0.0846
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> show #!12 models
> hide #!11 models
> hide #!8 models
> hide #!9 models
> show #!13 models
> hide #!12 models
> show #!11 models
> hide #!11 models
> close #12-13
> open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1711_volume_map.mrc
Opened cryosparc_P615_J1711_volume_map.mrc as #5, grid size 360,360,360, pixel
1.27, shown at level 0.0987, step 2, values float32
> open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1714_volume_map.mrc
Opened cryosparc_P615_J1714_volume_map.mrc as #6, grid size 360,360,360, pixel
1.27, shown at level 0.099, step 2, values float32
> hide #!6 models
> show #!6 models
> volume #5 step 1
> volume #6 step 1
> volume #5 level 0.08297
> show #!18 models
> hide #!5 models
> show #!5 models
> color #5 darkgrey
> color #5 near #18/A,B dist 6
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color zone #5 near #18/A,B distance 6
> ui tool show "Side View"
> save test.png width 3000 height 3000 supersample 3 transparentBackground
> true
[Repeated 1 time(s)]
> hide #!18 models
> show #!6 models
> hide #!5 models
> color #6 darkgrey
> color zone #6 near #18/A,B distance 6
> save J17114_class-3D_P5P1-dimer-1-reconstruct.png width 3000 height 3000
> supersample 3 transparentBackground true
> save J1714_class-3D_P5P1-dimer-1-reconstruct.png width 3000 height 3000
> supersample 3 transparentBackground true
> show #!5 models
> hide #!6 models
> save J1711_class-3D_P5P1-dimer-1-reconstruct.png width 3000 height 3000
> supersample 3 transparentBackground true
> view name diemr_1_close
> view list
Named views: bottom_overview, diemr_1_close, side_overview
> view side_overview
> show #!1 models
> hide #!5 models
> view #1 m
Expected an integer >= 1 or a keyword
> show #1 models
> show #!4 models
> show #4 models
> save J772_P5P1-dimer1-mask.png height 3000 width 3000 supersample 3
> transparentBackground true
> turn y 120
> show #!3 models
> hide #!4 models
> show #3 models
> show #2
> hide #!2 models
> show #!2 models
> hide #!3 models
> save J772_P5P1-dimer3-mask.png height 3000 width 3000 supersample 3
> transparentBackground true
> turn y 120
> show #!3 models
> hide #!2 models
> show #!2 models
> turn y 120
[Repeated 1 time(s)]
> hide #!3 models
> save J772_P5P1-dimer3-mask.png height 3000 width 3000 supersample 3
> transparentBackground true
> turn y 120
> show #!3 models
> hide #!2 models
> save J772_P5P1-dimer2-mask.png height 3000 width 3000 supersample 3
> transparentBackground true
> color #3 #168e781b models
> color #3 #168e7800 models
> color #3 #168e7880 models
> save J772_P5P1-dimer2-mask.png height 3000 width 3000 supersample 3
> transparentBackground true
> graphics silhouettes true width 8
> save J772_P5P1-dimer2-mask.png height 3000 width 3000 supersample 3
> transparentBackground true
> graphics silhouettes true width 16
> save J772_P5P1-dimer2-mask.png height 3000 width 3000 supersample 3
> transparentBackground true
> graphics silhouettes true width 32
> save J772_P5P1-dimer2-mask.png height 3000 width 3000 supersample 3
> transparentBackground true
> view list
Named views: bottom_overview, diemr_1_close, side_overview
> side_overview_P5P1_dimer_2
Unknown command: side_overview_P5P1_dimer_2
> view name side_overview_P5P1_dimer_2
> turn y 12
[Repeated 1 time(s)]
> turn y -12
[Repeated 1 time(s)]
> turn y 120
> hide #!3 models
> show #!4 models
> save J772_P5P1-dimer1-mask.png height 3000 width 3000 supersample 3
> transparentBackground true
> show #!3 models
> hide #!4 models
> show #!2 models
> hide #!3 models
> show #!4 models
> hide #!2 models
> view list
Named views: bottom_overview, diemr_1_close, side_overview,
side_overview_P5P1_dimer_2
> view side_overview
> save J772_P5P1-dimer1-mask.png height 3000 width 3000 supersample 3
> transparentBackground true
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!4 models
> undo
> redo
> view side_overview
> hide #!4 models
> turn y 120
> view name side_overview_P5P1_dimer_3
> save J772_P5P1-dimer3-mask.png height 3000 width 3000 supersample 3
> transparentBackground true
> graphics silhouettes true width 4
> hide #!2 models
> hide #!1 models
> show #!14 models
> show #!15 models
> hide #!14 models
> show #!16 models
> hide #!15 models
> show #!19 models
> hide #!16 models
> show #!15 models
> hide #!19 models
> show #!19 models
> hide #!15 models
> pwd
Current working directory is: /Users/lorenz.grundmann/VBC Dropbox/Group Folder
Haselbach/Projects/HERC1/Lorenz/P615_ZH027_ZH034-xlinked_P5P1_occupancy
> view list
Named views: bottom_overview, diemr_1_close, side_overview,
side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view diemr_1_close
> turn y 120
> view side_overview_P5P1_dimer_2
> view diemr_1_close
> view name dimer_1_close
> view delete diemer_1_close
> view list
Named views: bottom_overview, diemr_1_close, dimer_1_close, side_overview,
side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view dimer_1_close
> view dimer_2 close
Expected an objects specifier or a view name or a keyword
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> view list
Named views: bottom_overview, diemr_1_close, dimer_1_close, side_overview,
side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view side_overview_P5P1_dimer_3
> hide #!19 models
> show #!5 models
> show #!6 models
> hide #!5 models
> show #!8 models
> hide #!6 models
> show #!9 models
> hide #!8 models
> show #!10 models
> hide #!9 models
> show #!11 models
> hide #!10 models
> show #!10 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> show #!18 models
> hide #!10 models
> hide #!11 models
> show #!11 models
> show #!10 models
> hide #!11 models
> color #10,11 darkgrey
> show #!11 models
> hide #!10 models
> hide #!11 models
> color zone #11 near #18/J,I distance 6
> show #!11 models
> show #!10 models
> hide #!11 models
> show #!11 models
> hide #!10 models
> color #10,11 darkgrey
> color zone #11 near #18/J,I distance 4
> hide #!18 models
> show #!18 models
> hide #!18 models
> save test.png width 3000 height 3000 supersample 3 transparentBackground
> true
> view name dimer_3_close
> save J1846_class-3D_P5P1-dimer-3-reconstruct.png width 3000 height 3000
> supersample 3 transparentBackground true
> show #!10 models
> hide #!11 models
> show #!11 models
> hide #!10 models
> save J1846_class-3D_P5P1-dimer-3-reconstruct.png width 3000 height 3000
> supersample 3 transparentBackground true
> show #!10 models
> hide #!11 models
> save J1843_class-3D_P5P1-dimer-3-reconstruct.png width 3000 height 3000
> supersample 3 transparentBackground true
> hide #!10 models
> show #!8 models
> show #!9 models
> view list
Named views: bottom_overview, diemr_1_close, dimer_1_close, dimer_3_close,
side_overview, side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view side_overview_P5P1_dimer_2
> hide #!9 models
> show #!9 models
> hide #!8 models
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> show #!8 models
> color #8,9 darkgrey
> show #!18 models
> hide #!8 models
> color zone #10 near #18/K,L distance 6
> show #!10 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!10 models
> show #!9 models
> hide #!8 models
> show #!8 models
> color #10,11 darkgrey
> color zone #11 near #18/J,I distance 4
> hide #!9 models
> color zone #8 near #18/K,L distance 6
> hide #!18 models
> show #!9 models
> hide #!8 models
> show #!8 models
> save test.png width 3000 height 3000 supersample 3 transparentBackground
> true
> view name dimer_2_close
> hide #!9 models
> show #!9 models
> hide #!8 models
> save J1786_class-3D_P5P1-dimer-2-reconstruct.png width 3000 height 3000
> supersample 3 transparentBackground true
> show #!8 models
> hide #!9 models
> save J1783_class-3D_P5P1-dimer-2-reconstruct.png width 3000 height 3000
> supersample 3 transparentBackground true
> hide #!8 models
> show #!10 models
> show #!14 models
> hide #!10 models
> show #!15 models
> hide #!14 models
> hide #!15 models
> show #!16 models
> show #!14 models
> hide #!16 models
> show #!16 models
> hide #!14 models
> show #!19 models
> show #17 models
> hide #!16 models
> hide #17 models
> save analysis-cxs i t
Cannot determine format for 'analysis-cxs'
> save analysis.cxs includeMaps true
——— End of log from Mon Jan 19 11:45:42 2026 ———
opened ChimeraX session
> open
> /Users/lorenz.grundmann/Downloads/fold_herc2_1_1550_3mer/fold_herc2_1_1550_3mer_model_0.cif
Chain information for fold_herc2_1_1550_3mer_model_0.cif #7
---
Chain | Description
A B C | .
Computing secondary structure
> hide #7 models
> hide #!19 models
> show #!19 models
> open
> /Users/lorenz.grundmann/Downloads/fold_herc2_1_1550_3mer/fold_herc2_1_1550_3mer_model_0.cif
Chain information for fold_herc2_1_1550_3mer_model_0.cif #12
---
Chain | Description
A B C | .
Computing secondary structure
> hide #!19 models
> view #12 clip false
> color bychain
> open /Users/lorenz.grundmann/Downloads/fold_herc2/fold_herc2_model_0.cif
Chain information for fold_herc2_model_0.cif #13
---
Chain | Description
A | .
Computing secondary structure
> matchmaker #13 to #12/A
Computing secondary structure
[Repeated 1 time(s)] 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 fold_herc2_1_1550_3mer_model_0.cif, chain A (#12) with
fold_herc2_model_0.cif, chain A (#13), sequence alignment score = 7500.8
RMSD between 485 pruned atom pairs is 1.091 angstroms; (across all 1500 pairs:
22.343)
> rainbow #13
> open
> /Users/lorenz.grundmann/Downloads/fold_19s_base_paaf1/fold_19s_base_paaf1_job_request.json
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open
/Users/lorenz.grundmann/Downloads/fold_19s_base_paaf1/fold_19s_base_paaf1_job_request.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> open
> /Users/lorenz.grundmann/Downloads/fold_19s_base_paaf1/fold_19s_base_paaf1_model_0.cif
Chain information for fold_19s_base_paaf1_model_0.cif #20
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
G | .
H | .
I | .
J | .
K | .
L | .
> hide #12 models
> hide #13 models
> show #20 cartoons
Computing secondary structure
> hide #20 atoms
> hide #20 models
> show #20 models
> open
> /Users/lorenz.grundmann/Downloads/fold_19s_base_paaf1/fold_19s_base_paaf1_full_data_0.json
Opened AlphaFold PAE with values for 4971 residues and atoms
> color #20/K:856/L lime
> open "/Users/lorenz.grundmann/Downloads/cryosparc_P561_J448_009_volume_map
> (1).mrc"
Opened cryosparc_P561_J448_009_volume_map (1).mrc as #21, grid size
360,360,360, pixel 1.27, shown at level 0.0807, step 2, values float32
> hide #20 models
> view #21 clip false
> open
> /Users/lorenz.grundmann/Downloads/cryosparc_P561_J254_009_volume_map.mrc
Opened cryosparc_P561_J254_009_volume_map.mrc as #22, grid size 360,360,360,
pixel 1.27, shown at level 0.0788, step 2, values float32
> hide #!21 models
> volume #22 level 0.05311
> volume #22 step 1
> volume #22 level 0.08379
> show #!21 models
> hide #!22 models
> volume #21 step 1
> volume #21 level 0.1209
> open
> /Volumes/Herc/20241024_ZH027_Hek_Herc1_PSMC5_PAAF1/relion/J448/Refine3D/local_sampling_lp-12/run_class001.mrc
Opened run_class001.mrc as #23, grid size 360,360,360, pixel 1.27, shown at
level 0.00236, step 2, values float32
> volume #23 level 0.003573
> volume #23 step 1
> hide #!21 models
> volume #23 level 0.003573
> volume #23 level 0.004357
> color #28/1:372-734 light sky blue
> color #28/1:3420-3820 #350CED
> color #28/1:3996-4366 #90CED6
> color #28/1:4447-4840 #d31340ff
> color #28/1:2315-2379 palegreen
> color #28/1:1384-1399 #009193ff
> color #28/1:2747-2799 lime
> color #28/1:2975-3055 #EF6B11
> color #28/1:2075-2186 #F4EB45
> color #28/1:3297-3329 #CE3674
> close
> windowsize 1200 1200
> open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
> model/20260203_franekenmodel_new.pdb
Chain information for 20260203_franekenmodel_new.pdb #1
---
Chain | Description
1 | No description available
2 3 | No description available
A C E | No description available
B D F | No description available
> open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
> model/20260203_frankenmap.mrc
Opened 20260203_frankenmap.mrc as #2, grid size 360,360,360, pixel 1.27, shown
at level 0.14, step 2, values float32
> volume #2 step 1
> fitmap #1 inMap #2
Fit molecule 20260203_franekenmodel_new.pdb (#1) to map
20260203_frankenmap.mrc (#2) using 193662 atoms
average map value = 0.1852, steps = 124
shifted from previous position = 2.36
rotated from previous position = 2.79 degrees
atoms outside contour = 111278, contour level = 0.1401
Position of 20260203_franekenmodel_new.pdb (#1) relative to
20260203_frankenmap.mrc (#2) coordinates:
Matrix rotation and translation
0.99898431 -0.02740180 0.03577001 0.08643429
0.02805832 0.99944452 -0.01798280 -3.96522601
-0.03525738 0.01896818 0.99919824 4.42656013
Axis 0.37938688 0.72925970 0.56942592
Axis point 131.06536616 0.00000000 -2.28277335
Rotation angle (degrees) 2.79130992
Shift along axis -0.33828942
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show cartoons
> hide atoms
> show #!2 models
> fitmap #1 inMap #2
Fit molecule 20260203_franekenmodel_new.pdb (#1) to map
20260203_frankenmap.mrc (#2) using 193662 atoms
average map value = 0.1852, steps = 64
shifted from previous position = 0.019
rotated from previous position = 0.00619 degrees
atoms outside contour = 111364, contour level = 0.1401
Position of 20260203_franekenmodel_new.pdb (#1) relative to
20260203_frankenmap.mrc (#2) coordinates:
Matrix rotation and translation
0.99898711 -0.02743147 0.03566887 0.12837483
0.02808688 0.99944331 -0.01800537 -3.96190269
-0.03515510 0.01898896 0.99920145 4.41043263
Axis 0.38021682 0.72790771 0.57060104
Axis point 130.70040370 0.00000000 -3.28257276
Rotation angle (degrees) 2.78848325
Shift along axis -0.31849179
> close #1
> open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
> model/20260203_franekenmodel_new.pdb
Summary of feedback from opening
/Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
model/20260203_franekenmodel_new.pdb
---
warnings | Start residue of secondary structure not found: HELIX 114 114 ILE F 298 ILE F 300 1 3
Start residue of secondary structure not found: HELIX 115 115 SER F 303 LEU F
305 1 3
Start residue of secondary structure not found: HELIX 116 116 GLU F 322 HIS F
332 1 11
Start residue of secondary structure not found: HELIX 117 117 SER F 333 LYS F
335 1 3
Start residue of secondary structure not found: HELIX 118 118 LEU F 344 GLU F
349 1 6
756 messages similar to the above omitted
Ignored bad PDB record found on line 47792
RG F 297 190.126 173.141 191.732 1.00 53.47 N
Chain information for 20260203_franekenmodel_new.pdb
---
Chain | Description
1.1/1 | No description available
1.1/2 | No description available
1.1/3 | No description available
1.1/A 1.1/E | No description available
1.1/B 1.1/F | No description available
1.2/F | No description available
> close #1
> close #2
> open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
> model/20260203_franekenmodel_new.pdb
Summary of feedback from opening
/Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
model/20260203_franekenmodel_new.pdb
---
warnings | End residue of secondary structure not found: HELIX 305 305 VAL 3 2557 ARG 3 2573 1 17
Start residue of secondary structure not found: HELIX 306 306 VAL 3 3190 LEU 3
3197 1 8
Start residue of secondary structure not found: HELIX 307 307 SER 3 3203 LEU 3
3210 1 8
Start residue of secondary structure not found: HELIX 308 308 ILE 3 3218 ALA 3
3229 1 12
Start residue of secondary structure not found: HELIX 309 309 LEU 3 3263 ALA 3
3274 1 12
Start residue of secondary structure not found: HELIX 310 310 PRO 3 3278 THR 3
3297 1 20
412 messages similar to the above omitted
Ignored bad PDB record found on line 112037
566 293.184 107.305 203.880 1.00 92.87 H
Chain information for 20260203_franekenmodel_new.pdb
---
Chain | Description
1.1/1 | No description available
1.1/2 | No description available
1.1/3 | No description available
1.2/3 | No description available
1.1/A 1.1/C 1.1/E | No description available
1.1/B 1.1/D 1.1/F | No description available
Computing secondary structure
> hide #!1.2 models
> hide #!1.1 models
> close #1
> open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
> model/20260203_franekenmodel_new.pdb
Chain information for 20260203_franekenmodel_new.pdb #1
---
Chain | Description
1 | No description available
2 3 | No description available
A C E | No description available
B D F | No description available
> open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
> model/20260203_frankenmap.mrc
Opened 20260203_frankenmap.mrc as #2, grid size 360,360,360, pixel 1.27, shown
at level 0.14, step 2, values float32
> fitmap #1 inMap #2
Fit molecule 20260203_franekenmodel_new.pdb (#1) to map
20260203_frankenmap.mrc (#2) using 193662 atoms
average map value = 0.1852, steps = 124
shifted from previous position = 2.36
rotated from previous position = 2.79 degrees
atoms outside contour = 101671, contour level = 0.1401
Position of 20260203_franekenmodel_new.pdb (#1) relative to
20260203_frankenmap.mrc (#2) coordinates:
Matrix rotation and translation
0.99898431 -0.02740180 0.03577001 0.08643429
0.02805832 0.99944452 -0.01798280 -3.96522601
-0.03525738 0.01896818 0.99919824 4.42656013
Axis 0.37938688 0.72925970 0.56942592
Axis point 131.06536616 0.00000000 -2.28277335
Rotation angle (degrees) 2.79130992
Shift along axis -0.33828942
> volume #2 level 0.05999
> volume #2 step 1
> close
> open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
> model/20260203_frankemnmap.mrc
Opened 20260203_frankemnmap.mrc as #1, grid size 360,360,360, pixel 1.27,
shown at level 0.141, step 2, values float32
> open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
> model/20260203_frankemnmodel.pdb
Summary of feedback from opening
/Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
model/20260203_frankemnmodel.pdb
---
warnings | End residue of secondary structure not found: HELIX 142 142 ARG 3 4680 LEU 3 4692 1 13
Start residue of secondary structure not found: HELIX 143 143 ASP 3 4696 GLY 3
4705 1 10
Start residue of secondary structure not found: HELIX 144 144 MET 3 4706 TRP 3
4708 1 3
Start residue of secondary structure not found: HELIX 145 145 VAL 3 4712 LEU 3
4717 1 6
Start residue of secondary structure not found: HELIX 146 146 ALA 3 4720 CYS 3
4728 1 9
Start residue of secondary structure not found: HELIX 147 147 VAL 3 4735 LYS 3
4740 1 6
724 messages similar to the above omitted
Ignored bad PDB record found on line 55477
GLU 34689 256.307 357.171 212.206 1.00 65.82 C
Chain information for 20260203_frankemnmodel.pdb
---
Chain | Description
2.1/1 | No description available
2.1/3 | No description available
2.2/3 | No description available
2.1/A | No description available
2.1/B | No description available
2.1/E 2.1/F 2.1/G | No description available
> volume #1 step 1
> open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
> model/20260203_frankemnmodel.pdb
Chain information for 20260203_frankemnmodel.pdb #3
---
Chain | Description
1 8 9 | No description available
2 5 7 | No description available
3 4 6 | No description available
A I K | No description available
B J L | No description available
E F G | No description available
> hide #!1 models
> show #!1 models
> hide #!2 models
Cell requested for row 1 is out of bounds for table with 5 rows! Resizing
table model.
> close #2
> volume #1 level 0.008212
> hide atoms
> show cartoons
> volume #1 level 0.05603
> volume #1 level 0.1278
> volume #1 color #b2b2b281
> volume #1 level 0.2712
> open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
> model/20260203_frankemnmodel.pdb
Chain information for 20260203_frankemnmodel.pdb #2
---
Chain | Description
1 8 9 | No description available
2 5 7 | No description available
3 4 6 | No description available
A I K | No description available
B J L | No description available
E F G | No description available
> open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
> model/20260203_frankemnmap.mrc
Opened 20260203_frankemnmap.mrc as #4, grid size 360,360,360, pixel 1.27,
shown at level 0.141, step 2, values float32
> hide #!2 models
> hide #!1 models
> close #1-4
> open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
> model/20260203_frankemnmodel.pdb
Chain information for 20260203_frankemnmodel.pdb #1
---
Chain | Description
1 8 9 | No description available
2 5 7 | No description available
3 4 6 | No description available
A I K | No description available
B J L | No description available
E F G | No description available
> open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
> model/20260203_frankemnmap.mrc
Opened 20260203_frankemnmap.mrc as #2, grid size 360,360,360, pixel 1.27,
shown at level 0.141, step 2, values float32
> volume #2 step 1
> volume #2 level 0.05606
> hide #!1 models
> show #!1 models
> hide H
> style stick
Changed 192903 atom styles
> hide atoms
> show cartoons
> hide #!2 models
> hide #!1 models
> show #!1 models
> close #1
> open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
> model/20260203_frankemnmodel.pdb
Chain information for 20260203_frankemnmodel.pdb #1
---
Chain | Description
1 | No description available
2 3 | No description available
A C E | No description available
B D F | No description available
> show #!2 models
> hide atoms
> show cartoons
> hide #!2 models
> color #1/1 #BBBDBF
> color #1/2 #C691FF
> color #1/2 #6120AC
> color #1/3 #6120AC
> color #1/2 #C691FF
> color #1/1,-3:372-734 light sky blue
> color #1/1,-3:3420-3820 #350CED
> color #1/1,-3:3996-4366 #90CED6
> color #1/1,-3:4447-4840 #d31340ff
> color #1/1,-3:2315-2379 palegreen
> color #1/1,-3:1384-1399 #009193ff
> color #1/1,-3:2747-2799 lime
> color #1/1,-3:2975-3055 #EF6B11
> color #1/1,-3:2030-2190 #F4EB45
> color #1/1,-3:3297-3329 #CE3674
> color #1/1-3:372-734 light sky blue
> color #1/1-3:3420-3820 #350CED
> color #1/1-3:3996-4366 #90CED6
> color #1/1-3:4447-4840 #d31340ff
> color #1/1-3:2315-2379 palegreen
> color #1/1-3:1384-1399 #009193ff
> color #1/1-3:2747-2799 lime
> color #1/1-3:2975-3055 #EF6B11
> color #1/1-3:2030-2190 #F4EB45
> color #1/1-3:3297-3329 #CE3674
> color #1/A #363600
> color #1/B #ABAA00
> color #1/C #005A4A
> color #1/D #2CC9A6
> color #1/E #1F2A44
> color #1/F #5B7DBB
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> combine #1
> hide #!1 models
> show #!2 models
> volume #2 level 0.07655
> color zone #2 near #1 r 6
Expected a keyword
> color zone #2 near #1 distance 6
> hide #!2 models
> show #!2 models
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting soft
> hide #!2 models
> color #1/1 #BBBDBF
> color #1/2 #C691FF
> color #1/3 #6120AC
> color zone #2 near #1 distance 6
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!2 models
> color #1/a-c dark grey
> color zone #2 near #1 distance 6
> show #!2 models
> hide #!3 models
> hide #!2 models
> open
> /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/PSMC5-PAAF1-interface/20260114_P5P1_new-
> fit.cif
Summary of feedback from opening
/Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/PSMC5-PAAF1-interface/20260114_P5P1_new-
fit.cif
---
warnings | Unknown polymer entity '1' on line 166
Unknown polymer entity '2' on line 6052
Unknown polymer entity '3' on line 9979
Unknown polymer entity '4' on line 15357
Atom H is not in the residue template for LEU /B:137
Atom H is not in the residue template for GLU /C:370
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for 20260114_P5P1_new-fit.cif #4
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> open
> /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/PSMC5-PAAF1-interface/cryosparc_P615_J1927_014_volume_map.mrc
Opened cryosparc_P615_J1927_014_volume_map.mrc as #5, grid size 360,360,360,
pixel 1.27, shown at level 0.0844, step 2, values float32
> hide #!5 models
> hide #!4 models
> show #!4 models
> dssp #4
Computing secondary structure
> select #4/C,D 1
Expected a keyword
> changechains #4/C,D 1
Chain IDs of 530 residues changed
> windowsize 1100 1100
> color #4/1 #BBBDBF
> color #4/A #363600
> color #4/B #ABAA00
> show #!2 models
> hide #!2 models
> show #!5 models
> volume #5 step 1
> volume #5 level 0.2004
> color #5 #ffffb282 models
> color #4/1-3:372-734 light sky blue
> color #4/1-3:3420-3820 #350CED
> color #4/1-3:3996-4366 #90CED6
> color #4/1-3:4447-4840 #d31340ff
> color #4/1-3:2315-2379 palegreen
> color #4/1-3:1384-1399 #009193ff
> color #4/1-3:2747-2799 lime
> color #4/1-3:2975-3055 #EF6B11
> color #4/1-3:2030-2190 #F4EB45
> color #4/1-3:3297-3329 #CE3674
> color #5 near #4 tr 50
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #5 near #4
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color zone #5 near #4 trans 50
Expected a keyword
> color zone #5 near #4
> color zone #5 near #4 r 6
Expected a keyword
> color zone #5 near #4 distance 6
> transparency #5 50
> lighting soft
> color #4/1-3:372-734 light sky blue
> color #4/1-3:3420-3820 #350CED
> color #4/1-3:3996-4366 #90CED6
> color #4/1-3:4447-4840 #d31340ff
> color #4/1-3:2315-2379 palegreen
> color #4/1-3:1384-1399 #009193ff
> color #4/1-3:2747-2799 lime
> color #4/1-3:2975-3055 #EF6B11
> color #4/1-3:2030-2190 #F4EB45
> color #4/1-3:3297-3329 #CE3674
> show nucleic
> hide protein|solvent|H
> surface hidePatches
> style (protein|nucleic|solvent) & @@draw_mode=0 stick
Changed 385230 atom styles
> cartoon
> cartoon style modeHelix default arrows true arrowsHelix false arrowScale 2
> width 2 thickness 0.4 sides 12 divisions 20
> cartoon style ~(nucleic|strand) xsection round
> cartoon style (nucleic|strand) xsection rectangle
> cartoon style protein modeHelix default arrows false xsection round width 2
> thickness 1
> cartoon style nucleic xsection round width 1.6 thickness 1.6
> nucleotides stubs radius 0.5
> size stickRadius 0.3
Changed 407138 bond radii
> hide #!4 models
> show #!4 models
> view name P5P1_front
> select #4/A:373,381,384
50 atoms, 47 bonds, 3 residues, 1 model selected
> select #B/A:373,381,384
Expected an objects specifier or a keyword
> select #4/B:373,381,384
45 atoms, 42 bonds, 3 residues, 1 model selected
> select add #4/A:55,19,21,332,333,350,349
155 atoms, 147 bonds, 10 residues, 1 model selected
> select add #4/1:499,432,381,542,379,413,2176,2112,2123,2103
349 atoms, 334 bonds, 20 residues, 1 model selected
> show sel
> hide H
> color sel byhetero
> select add #4
17636 atoms, 17798 bonds, 1 pseudobond, 1170 residues, 2 models selected
> select subtract #4
Nothing selected
> select add #4/1:499,432,381,542,379,413,2176,2112,2123,2103
194 atoms, 187 bonds, 10 residues, 1 model selected
> select #4/A:373,381,384
50 atoms, 47 bonds, 3 residues, 1 model selected
> select #4/B:373,381,384
45 atoms, 42 bonds, 3 residues, 1 model selected
> select add #4/A:55,19,21,332,333,350,349
155 atoms, 147 bonds, 10 residues, 1 model selected
> name sel residues frozen
"sel" is reserved and cannot be redefined
> name residues sel frozen
"sel frozen": contains extra trailing text
> name frozen residues sel
> select add #4
17636 atoms, 17798 bonds, 1 pseudobond, 1170 residues, 2 models selected
> select subtract #4
Nothing selected
> hide resides
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide residues
> select add #4/1:499,432,381,542,379,413,2176,2112,2123,2103
194 atoms, 187 bonds, 10 residues, 1 model selected
> select #4/A:373,381,384
50 atoms, 47 bonds, 3 residues, 1 model selected
> select #4/B:373,381,384
45 atoms, 42 bonds, 3 residues, 1 model selected
> select add #4/A:55,19,21,332,333,350,349
155 atoms, 147 bonds, 10 residues, 1 model selected
> select add #4/1:499,432,381,542,379,413,2176,2112,2123,2103
349 atoms, 334 bonds, 20 residues, 1 model selected
> select #4/A:373,381,384
50 atoms, 47 bonds, 3 residues, 1 model selected
> select #4/B:373,381,384
45 atoms, 42 bonds, 3 residues, 1 model selected
> select add #4/A:55,19,21,332,333,350,349
155 atoms, 147 bonds, 10 residues, 1 model selected
> select add #4/1:499,432,381,542,379,413,2176,2112,2123,2103
349 atoms, 334 bonds, 20 residues, 1 model selected
> name frozen residues sel
> hide residues
> select add #4
17636 atoms, 17798 bonds, 1 pseudobond, 1170 residues, 2 models selected
> select subtract #4
Nothing selected
> view list
Named views: P5P1_front, bottom_overview, diemr_1_close, dimer_1_close,
dimer_2_close, dimer_3_close, side_overview, side_overview_P5P1_dimer_2,
side_overview_P5P1_dimer_3
> view P5P1_front
> cd "/Users/lorenz.grundmann/VBC Dropbox/Group Folder
> Haselbach/Projects/HERC1/Lorenz/ChimeraX_session/PSCM5-PAAF1-Herc1"
Current working directory is: /Users/lorenz.grundmann/VBC Dropbox/Group Folder
Haselbach/Projects/HERC1/Lorenz/ChimeraX_session/PSCM5-PAAF1-Herc1
> spng overview.png
> save overview.png width 3000 height 3000 supersample 3 transparentBackground
> true
> show residuesz
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show residues
> hdie H
Unknown command: hdie H
> hide H
> select #4/A:373,381,384
50 atoms, 47 bonds, 3 residues, 1 model selected
> select #4/B:373,381,384
45 atoms, 42 bonds, 3 residues, 1 model selected
> select add #4/1:499,432
88 atoms, 84 bonds, 5 residues, 1 model selected
> name frozen RLD1-PSMC5 sel
> hide residues
> show RLD1-PSMC5
> hide H
> select add #4
17636 atoms, 17798 bonds, 1 pseudobond, 1170 residues, 2 models selected
> view list
Named views: P5P1_front, bottom_overview, diemr_1_close, dimer_1_close,
dimer_2_close, dimer_3_close, side_overview, side_overview_P5P1_dimer_2,
side_overview_P5P1_dimer_3
> view P5P1_front
> select subtract #4
Nothing selected
> ui tool show "Side View"
> view name RLD1-P5-interface
> select add #4/B:373@OE2
1 atom, 1 residue, 1 model selected
> select add #4
17636 atoms, 17798 bonds, 1 pseudobond, 1170 residues, 4 models selected
> select add #5
17636 atoms, 17798 bonds, 1 pseudobond, 1170 residues, 6 models selected
> select subtract #5
17636 atoms, 17798 bonds, 1 pseudobond, 1170 residues, 2 models selected
> select subtract #4
Nothing selected
> hide #!5 models
> select add #4/B:373@OE2
1 atom, 1 residue, 1 model selected
> select add #4/1:499@NZ
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.3 dashes 4
> hide #4.2 models
> close #4.2
> pbond sel color grey radius 0.2 dashes 4
> close #4.2
> pbond sel color grey radius 0.2 dashes 4 name RLD1-P5
> select subtract #4/1:499@NZ
1 atom, 1 residue, 1 model selected
> select subtract #4/B:373@OE2
Nothing selected
> select add #4/1:499@NZ
1 atom, 1 residue, 1 model selected
> select add #4/B:381@OE2
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 name RLD1-P5
> select add #4/B:384@OE1
3 atoms, 3 residues, 1 model selected
> select add #4
17636 atoms, 17798 bonds, 3 pseudobonds, 1170 residues, 3 models selected
> select subtract #4
Nothing selected
> select #4/B:384@OE1
1 atom, 1 residue, 1 model selected
> select add #4/1:432@OH
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 name RLD1-P5
> close #4.2
> pbond sel color grey radius 0.2 dashes 4 name RLD1-P5 showDist true
> hide #4.2.1 models
> show #4.2.1 models
> select #4/B:381@OE2
1 atom, 1 residue, 1 model selected
> select add #4/1:499@NZ
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 name RLD1-P5 showDist true
> select #4/B:373@OE2
1 atom, 1 residue, 1 model selected
> select add #4/1:499@NZ
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 name RLD1-P5 showDist true
> close #4.2
Cell requested for row 5 is out of bounds for table with 8 rows! Resizing
table model.
> pbond sel color grey radius 0.2 dashes 4 name RLD1-P5 showDist true reveal
> true
Cell requested for row 0 is out of bounds for table with 8 rows! Resizing
table model.
> pbond sel color grey radius 0.2 dashes 4 reveal true name RLD1-P5 showDist
> true
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> label sel
> close #4.3
> select #4/B:373@OE2
1 atom, 1 residue, 1 model selected
> select add #4/1:499@NZ
2 atoms, 2 residues, 1 model selected
> label sel
> select #4/1:499@NZ
1 atom, 1 residue, 1 model selected
> select add #4/B:381@OE2
2 atoms, 2 residues, 1 model selected
> label sel
> view list
Named views: P5P1_front, RLD1-P5-interface, bottom_overview, diemr_1_close,
dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view P5P1_front
> view RLD1-P5-interface
> select subtract #4/1:499@NZ
1 atom, 1 residue, 1 model selected
> select #4/1:499@NZ
1 atom, 1 residue, 1 model selected
> select add #4/B:381@OE2
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 reveal true name RLD1-P5 showDist
> true
> hide #!4.2 models
> hide #4.3 models
> show #4.3 models
> hide #4.3 models
> show #4.3 models
> hide #4.3 models
> close #4.3
> show #!4.2 models
> select #4/B:384@OE1
1 atom, 1 residue, 1 model selected
> select add #4/1:432@OH
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 reveal true name RLD1-P5 showDist
> true
> select #4/B:373@OE2
1 atom, 1 residue, 1 model selected
> select add #4/1:499@NZ
2 atoms, 2 residues, 1 model selected
> select add #4/B:381@OE2
3 atoms, 3 residues, 1 model selected
> select add #4/B:381@OE1
4 atoms, 3 residues, 1 model selected
> select #4/B:381@OE1
1 atom, 1 residue, 1 model selected
> select #4/B:373@OE2
1 atom, 1 residue, 1 model selected
> select add #4/B:381@OE2
2 atoms, 2 residues, 1 model selected
> select add #4/B:384@OE1
3 atoms, 3 residues, 1 model selected
> select add #4/1:432@OH
4 atoms, 4 residues, 1 model selected
> label sel name RLD1-P5
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> label sel
> show #!2 models
> hide #!2 models
> show #!5 models
> select add #4
17636 atoms, 17798 bonds, 5 pseudobonds, 1170 residues, 5 models selected
> select subtract #4
Nothing selected
> spng RLD1-P5_interaction.png
> save RLD1-P5_interaction.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #4.2.1 models
> hide #4.3 models
> spng RLD1-P5_interaction.png
> save RLD1-P5_interaction.png width 3000 height 3000 supersample 3
> transparentBackground true
> show #4.2.1 models
> show #4.3 models
> spng RLD1-P5_interaction_labelled.png
> save RLD1-P5_interaction_labelled.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #!4.2 models
> hide #4.2.1 models
> hide #4.3 models
> show residues
> hide H
> show #4
> color #4 byhetero
> hide H
> select #5
4 models selected
> select #4/1:674@OD2
1 atom, 1 residue, 1 model selected
> hide #!5 models
> select add #4/A:41@NE2
2 atoms, 2 residues, 1 model selected
> select up
29 atoms, 27 bonds, 2 residues, 1 model selected
> select up
175 atoms, 174 bonds, 13 residues, 1 model selected
> select down
29 atoms, 27 bonds, 2 residues, 1 model selected
> select down
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 reveal true name test
> pbond sel color grey radius 0.2 dashes 4 reveal true name test showDist true
> select #4/A:50@OE1
1 atom, 1 residue, 1 model selected
> select add #4/1:691@OD1
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 reveal true name test showDist true
> select add #4/A:39@CG2
3 atoms, 3 residues, 1 model selected
> select add #4/1:674@OD2
4 atoms, 4 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 reveal true name test showDist true
Must specify exactly 2 atoms to form pseudobond between; you specified 4
> select #4/A:19
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #4/A:39@CG2
1 atom, 1 residue, 1 model selected
> select add #4/1:674@OD2
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 reveal true name test showDist true
> close #4.4
> view list
Named views: P5P1_front, RLD1-P5-interface, bottom_overview, diemr_1_close,
dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view P5P1_front
> hide #4
> show residues
> hdie H
Unknown command: hdie H
> hide H
> view P5P1_front
> select add #4
17636 atoms, 17798 bonds, 5 pseudobonds, 1170 residues, 5 models selected
> select subtract #4
Nothing selected
> select #4/1:381@OG
1 atom, 1 residue, 1 model selected
> select add #4/1:379@OG
2 atoms, 2 residues, 1 model selected
> select add #4/A:19@OE1
3 atoms, 3 residues, 1 model selected
> select add #4/A:21@OE2
4 atoms, 4 residues, 1 model selected
> select add #4/1:413@OH
5 atoms, 5 residues, 1 model selected
> select add #4/A:55@OE1
6 atoms, 6 residues, 1 model selected
> select add #4/1:542@NH1
7 atoms, 7 residues, 1 model selected
> show #4.2.1 models
> hide #4.2.1 models
> show #4.3 models
> hide #4.3 models
> label sel
> show #4.3 models
> select add #4
17636 atoms, 17798 bonds, 5 pseudobonds, 1170 residues, 5 models selected
> select subtract #4
Nothing selected
> show #!5 models
> color zone #5 near #4 distance 6
> combine #4
> color #5/1 #BBBDBF
> hide #4.1 models
> show #4.1 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> color #6/1 #BBBDBF
> hide #!5 models
> hide #!4 models
> color #6/1-3:372-734 light sky blue
> color #6/1-3:3420-3820 #350CED
> color #6/1-3:3996-4366 #90CED6
> color #6/1-3:4447-4840 #d31340ff
> color #6/1-3:2315-2379 palegreen
> color #6/1-3:1384-1399 #009193ff
> color #6/1-3:2747-2799 lime
> color #6/1-3:2975-3055 #EF6B11
> color #6/1-3:2030-2190 #F4EB45
> color #6/1-3:3297-3329 #CE3674
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> color #6 bychain
> color #6/1 #BBBDBF
> color #6/1-3:372-734 light sky blue
> color #6/1-3:3420-3820 #350CED
> color #6/1-3:3996-4366 #90CED6
> color #6/1-3:4447-4840 #d31340ff
> color #6/1-3:2315-2379 palegreen
> color #6/1-3:1384-1399 #009193ff
> color #6/1-3:2747-2799 lime
> color #6/1-3:2975-3055 #EF6B11
> color #6/1-3:2030-2190 #F4EB45
> color #6/1-3:3297-3329 #CE3674
> hide #6
> show nucleic
> hide protein|solvent|H
> surface hidePatches
> style (protein|nucleic|solvent) & @@draw_mode=0 stick
Changed 0 atom styles
> cartoon
> cartoon style modeHelix default arrows true arrowsHelix false arrowScale 2
> width 2 thickness 0.4 sides 12 divisions 20
> cartoon style ~(nucleic|strand) xsection round
> cartoon style (nucleic|strand) xsection rectangle
> cartoon style protein modeHelix default arrows false xsection round width 2
> thickness 1
> cartoon style nucleic xsection round width 1.6 thickness 1.6
> nucleotides stubs radius 0.5
> size stickRadius 0.3
Changed 424936 bond radii
> color #6 #7b68ee7e
> undo
> transparency #6 50
> transparency #6 50color #6 tr 50
Missing or invalid "percent" argument: Expected a number
> color #6 transparency 50
> show #!5 models
> show #!4 models
> color zone #5 near #6 distance 6
> transparency #5 50
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> shpw residues
Unknown command: shpw residues
> show residues
> hide H
> select add #4/1:381@OG
1 atom, 1 residue, 1 model selected
> select add #4/1:379@OG
2 atoms, 2 residues, 1 model selected
> select add #4/1:413@OH
3 atoms, 3 residues, 1 model selected
> select add #4/A:19@OE1
4 atoms, 4 residues, 1 model selected
> select add #4/A:21@OE1
5 atoms, 5 residues, 1 model selected
> select add #4/A:55@OE2
6 atoms, 6 residues, 1 model selected
> select add #4/1:542@NH1
7 atoms, 7 residues, 1 model selected
> select #4/1:542@NH1
1 atom, 1 residue, 1 model selected
> select add #4/A:55@OE2
2 atoms, 2 residues, 1 model selected
> select add #4/A:21@OE1
3 atoms, 3 residues, 1 model selected
> select add #4/A:19@OE1
4 atoms, 4 residues, 1 model selected
> select add #4/1:381@OG
5 atoms, 5 residues, 1 model selected
> select add #4/1:379@OG
6 atoms, 6 residues, 1 model selected
> select add #4/1:413@OH
7 atoms, 7 residues, 1 model selected
> select up
112 atoms, 106 bonds, 7 residues, 1 model selected
> name frozen sel RLD1-P1
Missing or invalid "objects" argument: invalid objects specifier
> name frozen RLD1-P1 sel
> select add #4
17636 atoms, 17798 bonds, 5 pseudobonds, 1170 residues, 5 models selected
> select subtract #4
Nothing selected
> show #!5 models
> color zone #5 near #6 distance 6
> transparency #5 50
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> color #6/B #ABAA00
> color zone #5 near #6 distance 6
> transparency #5 50
> show #!5 models
> color zone #5 near #6 distance 6
> transparency #5 50
> volume #5 level 0.1811
> transparency #5 50
> color zone #5 near #6 distance 6
> transparency #5 50
> hide #!5 models
> select clear
> select #4/1:381@OG
1 atom, 1 residue, 1 model selected
> select add #4/A:19@OE1
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 reveal true name RLD1-P1 showDist
> true
> select #4/1:379@OG
1 atom, 1 residue, 1 model selected
> select add #4/A:19@OE2
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 reveal true name RLD1-P1 showDist
> true
> select #4/1:413@OH
1 atom, 1 residue, 1 model selected
> select add #4/A:21@OE2
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 reveal true name RLD1-P1 showDist
> true
> select #4/A:55@OE2
1 atom, 1 residue, 1 model selected
> select add #4/1:542@NH1
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 reveal true name RLD1-P1 showDist
> true
> show #!5 models
> transparency #5 50
> color zone #5 near #6 distance 6
> transparency #5 50
> volume #5 level 0.2294
> color zone #5 near #6 distance 6
> transparency #5 50
> select add #4
17636 atoms, 17798 bonds, 9 pseudobonds, 1170 residues, 7 models selected
> select subtract #4
Nothing selected
> color zone #5 near #6 distance 6
> transparency #5 50
> spng RLD1-P1_interaction_labelled.png
> save RLD1-P1_interaction_labelled.png width 3000 height 3000 supersample 3
> transparentBackground true
> graphics silhouettes true width 4
> graphics silhouettes true width 8
> spng RLD1-P1_interaction_labelled.png
> save RLD1-P1_interaction_labelled.png width 3000 height 3000 supersample 3
> transparentBackground true
> graphics silhouettes true width 4
> graphics silhouettes true width 6
> view list
Named views: P5P1_front, RLD1-P5-interface, bottom_overview, diemr_1_close,
dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view P5P1_front
> spng RLD1-P1_interaction-1_labelled.png
> save RLD1-P1_interaction-1_labelled.png width 3000 height 3000 supersample 3
> transparentBackground true
> color zone #5 near #6 distance 6
> transparency #5 50
> select #4/1:728
11 atoms, 10 bonds, 1 residue, 1 model selected
> select resideus
Expected an objects specifier or a keyword
> select residues
Missing "residues" keyword's argument
> name list
RLD1-P1 [112 atoms, 212 bonds]
RLD1-PSMC5 [88 atoms, 168 bonds]
residues [349 atoms, 668 bonds]
> select residues
Missing "residues" keyword's argument
> show residues
> hide residues
> name
Missing or invalid "name" argument: Expected a text string
> select #4/A:373,381,384
50 atoms, 47 bonds, 3 residues, 1 model selected
> select #4/B:373,381,384
45 atoms, 42 bonds, 3 residues, 1 model selected
> select add #4/A:55,19,21,332,333,350,349
155 atoms, 147 bonds, 10 residues, 1 model selected
> select add #4/1:499,432,381,542,379,413,2176,2112,2123,2103
349 atoms, 334 bonds, 20 residues, 1 model selected
> select add #4/1:728
360 atoms, 344 bonds, 21 residues, 1 model selected
> show sel
> view name RLD1-P1_interaction-1
> select #4/A:19@OE2
1 atom, 1 residue, 1 model selected
> select add #4/1:728@HG
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 reveal true name RLD1-P1 showDist
> true
> view list
Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P5-interface,
bottom_overview, diemr_1_close, dimer_1_close, dimer_2_close, dimer_3_close,
side_overview, side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view P5P1_front
> show
> hide
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!4 models
> hide #!5 models
> color #6/B #ABAA00
> color #6/A #363600
> hide #!6 models
> select add #4/1:728
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #4/A:373,381,384
50 atoms, 47 bonds, 3 residues, 1 model selected
> select #4/B:373,381,384
45 atoms, 42 bonds, 3 residues, 1 model selected
> select add #4/A:55,19,21,332,333,350,349
155 atoms, 147 bonds, 10 residues, 1 model selected
> select add #4/1:499,432,381,542,379,413,2176,2112,2123,2103
349 atoms, 334 bonds, 20 residues, 1 model selected
> show #!6 models
> hide #!6 models
> show #!4 models
> name frozen residues sel
> view list
Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P5-interface,
bottom_overview, diemr_1_close, dimer_1_close, dimer_2_close, dimer_3_close,
side_overview, side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view RLD1-P1_interaction-1
> show residues
> hide H
> select add #4
17636 atoms, 17798 bonds, 10 pseudobonds, 1170 residues, 7 models selected
> select subtract #4
Nothing selected
> show #!5 models
> select add #4/1:499,432,381,542,379,413,2176,2112,2123,2103
194 atoms, 187 bonds, 10 residues, 1 model selected
> select #4/A:373,381,384
50 atoms, 47 bonds, 3 residues, 1 model selected
> select #4/B:373,381,384
45 atoms, 42 bonds, 3 residues, 1 model selected
> select add #4/A:55,19,21,332,333,350,349
155 atoms, 147 bonds, 10 residues, 1 model selected
> select add #4/1:728
166 atoms, 157 bonds, 11 residues, 1 model selected
> name frozen residues sel
> show residues
> hide H
> select #4/A:19@OE2
1 atom, 1 residue, 1 model selected
> select add #4/1:728@OG
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 reveal true name RLD1-P1 showDist
> true
> view list
Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P5-interface,
bottom_overview, diemr_1_close, dimer_1_close, dimer_2_close, dimer_3_close,
side_overview, side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view RLD1-P1_interaction-1
> color zone #5 near #6 distance 6
> transparency #5 50
> select add #4
17636 atoms, 17798 bonds, 11 pseudobonds, 1170 residues, 7 models selected
> select subtract #4
Nothing selected
> spng RLD1-P1_interaction-1_labelled.png
> save RLD1-P1_interaction-1_labelled.png width 3000 height 3000 supersample 3
> transparentBackground true
> view RLD1-P1_interaction-1
[Repeated 1 time(s)]
> color zone #5 near #6 distance 6
> transparency #5 50
> spng RLD1-P1_interaction-2_labelled.png
> save RLD1-P1_interaction-2_labelled.png width 3000 height 3000 supersample 3
> transparentBackground true
> transparency #5 50
> color zone #5 near #6 distance 6
> transparency #5 50
> color zone #5 near #6 distance 6
> transparency #5 50
> spng RLD1-P1_interaction-2_labelled.png
> save RLD1-P1_interaction-2_labelled.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #4.3 models
> hide #4.4.1 models
> color zone #5 near #6 distance 6
> transparency #5 50
> spng RLD1-P1_interaction-2.png
> save RLD1-P1_interaction-2.png width 3000 height 3000 supersample 3
> transparentBackground true
> view list
Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P5-interface,
bottom_overview, diemr_1_close, dimer_1_close, dimer_2_close, dimer_3_close,
side_overview, side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view name RLD1-P1_interaction-2
> view RLD1-P1_interaction-1
> transparency #5 50
> color zone #5 near #6 distance 6
> transparency #5 50
> spng RLD1-P1_interaction-1.png
> save RLD1-P1_interaction-1.png width 3000 height 3000 supersample 3
> transparentBackground true
> view list
Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
RLD1-P5-interface, bottom_overview, diemr_1_close, dimer_1_close,
dimer_2_close, dimer_3_close, side_overview, side_overview_P5P1_dimer_2,
side_overview_P5P1_dimer_3
> view RLD1-P1_interaction-2
> view name RLD1-P1_interaction-1
> color zone #5 near #6 distance 6
> transparency #5 50
> spng RLD1-P1_interaction-2.png
> save RLD1-P1_interaction-2.png width 3000 height 3000 supersample 3
> transparentBackground true
> show #4.4.1 models
> show #4.3 models
> spng RLD1-P1_interaction-2_labelled.png
> save RLD1-P1_interaction-2_labelled.png width 3000 height 3000 supersample 3
> transparentBackground true
> color zone #5 near #6 distance 6
> transparency #5 50
> spng RLD1-P1_interaction-2_labelled.png
> save RLD1-P1_interaction-2_labelled.png width 3000 height 3000 supersample 3
> transparentBackground true
> view list
Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
RLD1-P5-interface, bottom_overview, diemr_1_close, dimer_1_close,
dimer_2_close, dimer_3_close, side_overview, side_overview_P5P1_dimer_2,
side_overview_P5P1_dimer_3
> view P5P1_front
> volume #5 level 0.1714
> hide #!5 models
> show #!5 models
> volume #5 level 0.2488
> volume #5 level 0.2004
> select #5
4 models selected
> hide #!5 models
> select #4/A:349@NE2
1 atom, 1 residue, 1 model selected
> select add #4/1:2176@OH
2 atoms, 2 residues, 1 model selected
> select up
38 atoms, 37 bonds, 2 residues, 1 model selected
> name frozen SPRY-P1_1
Missing or invalid "objects" argument: empty atom specifier
> name frozen SPRY-P1_1 sel
> hide residues
> show SPRY-P1_1
> hide H
> hide residues
> name list
RLD1-P1 [112 atoms, 212 bonds]
RLD1-PSMC5 [88 atoms, 168 bonds]
SPRY-P1_1 [38 atoms, 74 bonds]
residues [166 atoms, 314 bonds]
> hide al
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide al
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide all
> show residues
> hide residues
> select #4/B:373,381,384
45 atoms, 42 bonds, 3 residues, 1 model selected
> select add #4/A:55,19,21,332,333,350,349
155 atoms, 147 bonds, 10 residues, 1 model selected
> select add #4/1:728
166 atoms, 157 bonds, 11 residues, 1 model selected
> select add #4/1:499,432,381,542,379,413,2176,2112,2123,2103
360 atoms, 344 bonds, 21 residues, 1 model selected
> name frozen residues sel
> show residues
> hide residues
> show SPRY-P1_1
> hide H
> show #!5 models
> select add #4
17636 atoms, 17798 bonds, 11 pseudobonds, 1170 residues, 7 models selected
> select subtract #4
Nothing selected
> hide #!5 models
> select #4/A:349@NE2
1 atom, 1 residue, 1 model selected
> select add #4/1:2176@OH
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 reveal true name SPRY-P1-1 showDist
> true
> label sel
> show #!5 models
> color zone #5 near #6 distance 6
> transparency #5 50
> spng SPRY-P1_1_labelled.png
> save SPRY-P1_1_labelled.png width 3000 height 3000 supersample 3
> transparentBackground true
> select add #4
17636 atoms, 17798 bonds, 12 pseudobonds, 1170 residues, 9 models selected
> select subtract #4
Nothing selected
> color zone #5 near #6 distance 6
> transparency #5 50
> spng SPRY-P1_1_labelled.png
> save SPRY-P1_1_labelled.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #4.4.1 models
> hide #4.3 models
> spng SPRY-P1_1.png
> save SPRY-P1_1.png width 3000 height 3000 supersample 3
> transparentBackground true
> color zone #5 near #6 distance 6
> transparency #5 50
> color zone #5 near #6 distance 6
> transparency #5 50
> spng SPRY-P1_1.png
> save SPRY-P1_1.png width 3000 height 3000 supersample 3
> transparentBackground true
> show #4.4.1 models
> hide #4.4.1 models
> show #4.3 models
> color zone #5 near #6 distance 6
> transparency #5 50
> spng SPRY-P1_1_labelled.png
> save SPRY-P1_1_labelled.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #4.3 models
> hide #4.5.1 models
> spng SPRY-P1_1.png
> save SPRY-P1_1.png width 3000 height 3000 supersample 3
> transparentBackground true
> view name SPRY-P1_1
> show residues
> hide H
> name list
RLD1-P1 [112 atoms, 212 bonds]
RLD1-PSMC5 [88 atoms, 168 bonds]
SPRY-P1_1 [38 atoms, 74 bonds]
residues [360 atoms, 688 bonds]
> hide SPRY-P1_1
> volume #5 level 0.1811
> color zone #5 near #6 distance 6
> transparency #5 50
> hide #!5 models
> hide SPRY-P1_2
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> view name SPRY-P1_2
> show #!5 models
> select #4/A:332@NH1
1 atom, 1 residue, 1 model selected
> select add #4/1:2123@OE1
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 reveal true name SPRY-P1-2 showDist
> true
> select #4/1:2123@OE2
1 atom, 1 residue, 1 model selected
> select add #4/A:333@OD1
2 atoms, 2 residues, 1 model selected
> select #4/1:2103@NH2
1 atom, 1 residue, 1 model selected
> select add #4/A:333@OD2
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 reveal true name SPRY-P1-2 showDist
> true
> select #4/1:2112@NH1
1 atom, 1 residue, 1 model selected
> select add #4/A:350@OD1
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 reveal true name SPRY-P1-2 showDist
> true
> select #4/1:2103@NH1
1 atom, 1 residue, 1 model selected
> select add #4/A:350@OD1
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 reveal true name SPRY-P1-2 showDist
> true
> hide #!5 models
> select add #4/1:2112@NH1
3 atoms, 3 residues, 1 model selected
> select add #4/A:333@OD2
4 atoms, 4 residues, 1 model selected
> select add #4/1:2123@OE2
5 atoms, 5 residues, 1 model selected
> select add #4/A:332@NH1
6 atoms, 6 residues, 1 model selected
> select up
111 atoms, 106 bonds, 6 residues, 1 model selected
> name frozen SPRY-P1_12 sel
> name frozen SPRY-P1_2 sel
> name remove SPRY-P1_2
> name remove SPRY-P1_12
> name frozen SPRY-P1_2 sel
> show #!5 models
> volume #5 level 0.1908
> color zone #5 near #6 distance 6
> transparency #5 50
> select add #4
17636 atoms, 17798 bonds, 16 pseudobonds, 1170 residues, 11 models selected
> select subtract #4
Nothing selected
> spng SPRY-P1_2_labelled.png
> save SPRY-P1_2_labelled.png width 3000 height 3000 supersample 3
> transparentBackground true
> select #4/1:2103@NH2
1 atom, 1 residue, 1 model selected
> select #4/A:350@OD1
1 atom, 1 residue, 1 model selected
> select add #4/1:2103@NH2
2 atoms, 2 residues, 1 model selected
> select add #5
2 atoms, 2 residues, 5 models selected
> select subtract #5
2 atoms, 2 residues, 1 model selected
> hide #!5 models
> select add #4/1:2112@NH1
3 atoms, 3 residues, 1 model selected
> select add #4/1:2112@NH2
4 atoms, 3 residues, 1 model selected
> select add #4/A:333@OD2
5 atoms, 4 residues, 1 model selected
> select add #4/1:2123@OE1
6 atoms, 5 residues, 1 model selected
> select add #4/A:332@NH1
7 atoms, 6 residues, 1 model selected
> label sel
> show #4.3 models
> hide #4.3 models
> show #4.3 models
> hide #!4.6 models
> show #!4.6 models
> hide #4.3 models
> show #4.3 models
> hide #4.3 models
> show #4.3 models
> hide #!4.6 models
> show #!4.6 models
> show #!5 models
> color zone #5 near #6 distance 6
> transparency #5 50
> spng SPRY-P1_2_labelled.png
> save SPRY-P1_2_labelled.png width 3000 height 3000 supersample 3
> transparentBackground true
> select add #4
17636 atoms, 17798 bonds, 16 pseudobonds, 1170 residues, 11 models selected
> select subtract #4
Nothing selected
> spng SPRY-P1_2_labelled.png
> save SPRY-P1_2_labelled.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #!4.6 models
> show #!4.6 models
> hide #4.6.1 models
> hide #4.3 models
> spng SPRY-P1_2.png
> save SPRY-P1_2.png width 3000 height 3000 supersample 3
> transparentBackground true
> save 20260203_interactions.cxs
> view list
Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
RLD1-P5-interface, SPRY-P1_1, SPRY-P1_2, bottom_overview, diemr_1_close,
dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view P5P1_front
> volume #5 level 0.2294
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!5 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!2 models
> show #!3 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> show #!1 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> show #!3 models
> hide #!1 models
> show #!2 models
> view list
Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
RLD1-P5-interface, SPRY-P1_1, SPRY-P1_2, bottom_overview, diemr_1_close,
dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view P5P1_front
> vop copy #2
Opened 20260203_frankemnmap.mrc copy as #7, grid size 360,360,360, pixel 1.27,
shown at step 1, values float32
> hide #!3 models
> show #!3 models
> color zone #7 near #3 distance 6
> hide #!7 models
> show #!7 models
> hide #!4.6 models
> hide #!7 models
> show #!7 models
> hide #4.1 models
> hide #!3 models
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/lorenz.grundmann/Desktop/movie1.mp4
Movie saved to /Users/lorenz.grundmann/Desktop/movie1.mp4
> view #7 clip false
> save /Users/lorenz.grundmann/Desktop/image1.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/lorenz.grundmann/Desktop/movie2.mp4
Movie saved to /Users/lorenz.grundmann/Desktop/movie2.mp4
> view list
Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
RLD1-P5-interface, SPRY-P1_1, SPRY-P1_2, bottom_overview, diemr_1_close,
dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view bottom_overview
> spng bottom.png
> save bottom.png width 3000 height 3000 supersample 3 transparentBackground
> true
> view side_overview_P5P1_dimer_2
> view side_overview_P5P1_dimer_3
> view side_overview
> spng side.png
> save side.png width 3000 height 3000 supersample 3 transparentBackground
> true
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/lorenz.grundmann/Desktop/movie3.mp4
Movie saved to /Users/lorenz.grundmann/Desktop/movie3.mp4
> hide #!7 models
> show #!3 models
> graphics silhouettes true width 4
> view list
Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
RLD1-P5-interface, SPRY-P1_1, SPRY-P1_2, bottom_overview, diemr_1_close,
dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view P5P1_front
> hide #!4.2 models
> show #!4.2 models
> hide #!4.2 models
> show #!4.2 models
> show #4.1 models
> hide #!4 models
> mathc #3 to #4
Unknown command: mathc #3 to #4
> matchmaker #3 to #4
Computing secondary structure
[Repeated 1 time(s)] 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 20260114_P5P1_new-fit.cif, chain A (#4) with copy of
20260203_frankemnmodel.pdb, chain A (#3), sequence alignment score = 2024.9
RMSD between 392 pruned atom pairs is 0.320 angstroms; (across all 392 pairs:
0.320)
> hide #4.1 models
> show #4.1 models
> hide #!3 models
> show #!3 models
> hide #4.1 models
> show #4.1 models
> hide #!4 models
> view list
Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
RLD1-P5-interface, SPRY-P1_1, SPRY-P1_2, bottom_overview, diemr_1_close,
dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view side_overview
> hide #3/2 cartoons
> hide #3/C-f
> hide #3/C-F
> hide #3/C-F cartoons
> hide #3/3:370-738
> hide #3/3:370-738 cartoons
> color #3/1-3:3996-4366 #0437FF
> undo
> color #3/1-3:3420-3820 #0437FF
[Repeated 1 time(s)]
> show #!2 models
> hide #!2 models
> show #!7 models
> hide #!3 models
> show #!3 models
> hide #!7 models
> show #!7 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!3 models
> color zone #7 near #3 distance 6
> hide #!7 models
> show #!2 models
> hide #!3 models
> view list
Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
RLD1-P5-interface, SPRY-P1_1, SPRY-P1_2, bottom_overview, diemr_1_close,
dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view side_overview
> side.png
Unknown command: side.png
> spng side.png
> save side.png width 3000 height 3000 supersample 3 transparentBackground
> true
> view bottom_overview
> spng bottom.png
> save bottom.png width 3000 height 3000 supersample 3 transparentBackground
> true
> hide #!2 models
> color #1/A #363600
> color #1/B #ABAA00
> color #1/E #005A4A
> color #1/F #2CC9A6
> color #1/C #1F2A44
> color #1/D #5B7DBB
> show #!1 models
> color #3/A #363600
> color #3/B #ABAA00
> color #3/E #005A4A
> color #3/F #2CC9A6
> color #3/C #3F2A44
> color #3/D #5B7DBB
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!1 models
> color zone #2 near #1 distance 6
> view list
Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
RLD1-P5-interface, SPRY-P1_1, SPRY-P1_2, bottom_overview, diemr_1_close,
dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view bottom_overview
> spng bottom.png
> save bottom.png width 3000 height 3000 supersample 3 transparentBackground
> true
Cell requested for row 0 is out of bounds for table with 17 rows! Resizing
table model.
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> view side_overview
> spng side.png
> save side.png width 3000 height 3000 supersample 3 transparentBackground
> true
> hide #!2 models
> show #!1 models
> show #!7 models
> hide #!7 models
> hide #!1 models
> show #!1 models
> show #!3 models
> hide #!1 models
> view list
Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
RLD1-P5-interface, SPRY-P1_1, SPRY-P1_2, bottom_overview, diemr_1_close,
dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view side_overview
> view list
Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
RLD1-P5-interface, SPRY-P1_1, SPRY-P1_2, bottom_overview, diemr_1_close,
dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view side_overview
> hide #2 cartoons
> hide #3/2 cartoons
> hide #3/3 cartoons
> view list
Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
RLD1-P5-interface, SPRY-P1_1, SPRY-P1_2, bottom_overview, diemr_1_close,
dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view side_overview
[Repeated 1 time(s)]
> spng protomer_P5P1.png
> save protomer_P5P1.png width 3000 height 3000 supersample 3
> transparentBackground true
> turn z 180
[Repeated 3 time(s)]
> turn y 180
> spng protomer_P5P1_180.png
> save protomer_P5P1_180.png width 3000 height 3000 supersample 3
> transparentBackground true
> view list
Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
RLD1-P5-interface, SPRY-P1_1, SPRY-P1_2, bottom_overview, diemr_1_close,
dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view side_overview
> view side_overview_P5P1_dimer_3
> view side_overview
> shpw #3/3 cartoon
Unknown command: shpw #3/3 cartoon
> show #3/3 cartoons
> spng protomer_2_P5P1_180.png
> save protomer_2_P5P1_180.png width 3000 height 3000 supersample 3
> transparentBackground true
> save 20260203_interactions.cxs includeMaps true
——— End of log from Tue Feb 3 16:26:41 2026 ———
> view name session-start
opened ChimeraX session
> windowsize 1100 1000
> windowsize 1000 1000
> windowsize 9000 9000
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/lorenz.grundmann/VBC Dropbox/Group Folder
> Haselbach/Projects/HERC1/Lorenz/ChimeraX_session/PSCM5-PAAF1-Herc1/20260203_interactions.cxs"
Opened 20260203_frankemnmap.mrc as #2, grid size 360,360,360, pixel 1.27,
shown at level 0.0765, step 1, values float32
Opened cryosparc_P615_J1927_014_volume_map.mrc as #5, grid size 360,360,360,
pixel 1.27, shown at level 0.229, step 1, values float32
Opened 20260203_frankemnmap.mrc copy as #7, grid size 360,360,360, pixel 1.27,
shown at level 0.0765, step 1, values float32
Log from Tue Feb 3 16:26:41 2026UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/lorenz.grundmann/VBC Dropbox/Group Folder
> Haselbach/Projects/HERC1/Lorenz/P615_ZH027_ZH034-xlinked_P5P1_occupancy/analysis.cxs"
Opened cryosparc_P615_J1783_volume_map.mrc as #8, grid size 360,360,360, pixel
1.27, shown at level 0.0846, step 1, values float32
Opened cryosparc_P615_J1786_volume_map.mrc as #9, grid size 360,360,360, pixel
1.27, shown at level 0.0846, step 1, values float32
Opened cryosparc_P615_J1843_volume_map.mrc as #10, grid size 360,360,360,
pixel 1.27, shown at level 0.0846, step 1, values float32
Opened cryosparc_P615_J1846_volume_map.mrc as #11, grid size 360,360,360,
pixel 1.27, shown at level 0.0846, step 1, values float32
Opened cryosparc_P615_J1930_volume_map.mrc as #14, grid size 360,360,360,
pixel 1.27, shown at level 0.09, step 1, values float32
Opened cryosparc_P615_J1932_volume_map.mrc as #15, grid size 360,360,360,
pixel 1.27, shown at level 0.09, step 1, values float32
Opened cryosparc_P615_J1934_volume_map.mrc as #16, grid size 360,360,360,
pixel 1.27, shown at level 0.09, step 1, values float32
Opened cryosparc_P615_J1936_volume_map.mrc as #19, grid size 360,360,360,
pixel 1.27, shown at level 0.09, step 1, values float32
Opened cryosparc_P615_J772_011_volume_map.mrc as #1, grid size 360,360,360,
pixel 1.27, shown at level 0.099, step 1, values float32
Opened cryosparc_P615_J528_mask.mrc as #2, grid size 240,240,240, pixel 1.9,
shown at level 0.5, step 1, values float32
Opened cryosparc_P615_J526_mask (1).mrc as #3, grid size 240,240,240, pixel
1.9, shown at level 0.5, step 1, values float32
Opened cryosparc_P615_J453_mask (1).mrc as #4, grid size 360,360,360, pixel
1.27, shown at level 0.5, step 2, values float32
Opened cryosparc_P615_J1711_volume_map.mrc as #5, grid size 360,360,360, pixel
1.27, shown at level 0.083, step 1, values float32
Opened cryosparc_P615_J1714_volume_map.mrc as #6, grid size 360,360,360, pixel
1.27, shown at level 0.099, step 1, values float32
Log from Mon Jan 19 11:45:42 2026 Startup Messages
---
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr bundle with that from OME-Zarr bundle
Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Volumes/Herc/20241024_ZH027_Hek_Herc1_PSMC5_PAAF1/relion/J448/Refine3D/lp-12/run_class001.mrc
Opened run_class001.mrc as #1, grid size 360,360,360, pixel 1.27, shown at
level 0.00123, step 2, values float32
> volume #1 level 0.00391
> volume #1 step 1
> volume #1 level 0.004416
> open
> /Users/lorenz.grundmann/Downloads/cryosparc_P713_J541_002_volume_map.mrc
Opened cryosparc_P713_J541_002_volume_map.mrc as #2, grid size 256,256,256,
pixel 0.951, shown at level 0.0567, step 1, values float32
> hide #!1 models
> view #2 clip false
> volume #2 level 0.1409
> open
> /Users/lorenz.grundmann/Downloads/fold_herc1_zinc/fold_herc1_zinc_model_0.cif
Summary of feedback from opening
/Users/lorenz.grundmann/Downloads/fold_herc1_zinc/fold_herc1_zinc_model_0.cif
---
note | Fetching CCD ZN from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif
Chain information for fold_herc1_zinc_model_0.cif #3
---
Chain | Description
A | .
> hide #!2 models
> select /A:372-739
2719 atoms, 2772 bonds, 368 residues, 1 model selected
> show sequence sel
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 3/A
No active region
> select /A:739
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:420-739
2348 atoms, 2392 bonds, 320 residues, 1 model selected
> select /A:372-739
2719 atoms, 2772 bonds, 368 residues, 1 model selected
> select /A:1987-2027
336 atoms, 339 bonds, 41 residues, 1 model selected
> select /A:2027-2358
2603 atoms, 2653 bonds, 332 residues, 1 model selected
> select /A:2027-2193
1304 atoms, 1335 bonds, 167 residues, 1 model selected
> open
> /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/relion/J772_preP5P1-class_consensus_C3-relaxed/Class3D/dimer_2_iAlign_cl3_blush/run_it025_class001.mrc
Opened run_it025_class001.mrc as #4, grid size 360,360,360, pixel 1.27, shown
at level 2.54e-06, step 2, values float32
> open
> /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/relion/J772_preP5P1-class_consensus_C3-relaxed/Class3D/dimer_2_iAlign_cl3_blush/run_it025_class002.mrc
Opened run_it025_class002.mrc as #5, grid size 360,360,360, pixel 1.27, shown
at level 2.38e-06, step 2, values float32
> open
> /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/relion/J772_preP5P1-class_consensus_C3-relaxed/Class3D/dimer_2_iAlign_cl3_blush/run_it025_class003.mrc
Opened run_it025_class003.mrc as #6, grid size 360,360,360, pixel 1.27, shown
at level 8.79e-07, step 2, values float32
> hide #3 models
> view #5 clip false
> volume #4 level 0.006078
> volume #5 level 0.005325
> volume #6 level 0.004012
> open
> /Volumes/Herc/20230421_Herc_WT/model_building/model_finalisation/RLD1_PCNA/phenix/RealSpaceRefine_2/20250108_RLDs-
> fitted_real_space_refined_002.cif
Summary of feedback from opening
/Volumes/Herc/20230421_Herc_WT/model_building/model_finalisation/RLD1_PCNA/phenix/RealSpaceRefine_2/20250108_RLDs-
fitted_real_space_refined_002.cif
---
warnings | Skipping chem_comp category: Missing column 'type' near line 510
Missing entity information. Treating each chain as a separate entity.
Invalid residue range for struct_conf "1": invalid chain "1", near line 138
Invalid residue range for struct_conf "2": invalid chain "1", near line 139
Invalid residue range for struct_conf "3": invalid chain "1", near line 140
Invalid residue range for struct_conf "4": invalid chain "1", near line 141
Invalid residue range for struct_conf "5": invalid chain "1", near line 142
31 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "1 1": invalid chain "1", near line
392
Invalid sheet range for struct_sheet_range "2 1": invalid chain "1", near line
393
Invalid sheet range for struct_sheet_range "3 1": invalid chain "1", near line
394
Invalid sheet range for struct_sheet_range "4 1": invalid chain "1", near line
395
Invalid sheet range for struct_sheet_range "5 1": invalid chain "1", near line
396
112 messages similar to the above omitted
Atom H1 is not in the residue template for VAL /1:512
Atom H1 is not in the residue template for GLY /1:633
Atom H1 is not in the residue template for THR /1:665
Atom H1 is not in the residue template for SER /1:675
Atom H3 is not in the residue template for PRO /1:705
Atom H is not in the residue template for LYS /1:1384
Atom H1 is not in the residue template for VAL /2:512
Atom H1 is not in the residue template for GLY /2:633
Atom H1 is not in the residue template for THR /2:665
Too many hydrogens missing from residue template(s) to warn about
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for 20250108_RLDs-fitted_real_space_refined_002.cif #7
---
Chain | Description
1 2 | No description available
3 | No description available
Ba Bb Bc | No description available
> hide #!6 models
> show sequence #7/1
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> sequence chain #7/1
Alignment identifier is 7/1
> select #7/1:1399
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #7/1
5120 atoms, 5166 bonds, 7 pseudobonds, 344 residues, 2 models selected
> open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1783_volume_map.mrc
Opened cryosparc_P615_J1783_volume_map.mrc as #8, grid size 360,360,360, pixel
1.27, shown at level 0.101, step 2, values float32
> open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1786_volume_map.mrc
Opened cryosparc_P615_J1786_volume_map.mrc as #9, grid size 360,360,360, pixel
1.27, shown at level 0.0998, step 2, values float32
> hide #!7 models
> volume #8 level 0.07925
> volume #9 level 0.08883
> volume #9 step 1
> volume #8 step 1
> volume #9 level 0.09891
> volume #9 level 0.08782
> open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1843_volume_map.mrc
Opened cryosparc_P615_J1843_volume_map.mrc as #10, grid size 360,360,360,
pixel 1.27, shown at level 0.0985, step 2, values float32
> hide #!8 models
> hide #!9 models
> open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1846_volume_map.mrc
Opened cryosparc_P615_J1846_volume_map.mrc as #11, grid size 360,360,360,
pixel 1.27, shown at level 0.103, step 2, values float32
> hide #!10 models
> show #!10 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> volume #11 step 1
> volume #10 step 1
> show #!11 models
> hide #!11 models
> show #!11 models
> volume #10 level 0.07064
> volume #10 level 0.09529
> show #!8 models
> show #!9 models
> hide #!10 models
> show #!10 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!10 models
> hide #!11 models
> volume #9 level 0.09589
> volume #8 level 0.08615
> volume #9 level 0.06767
> volume #10 level 0.0835
> volume #9 level 0.08178
> show #!11 models
> hide #!10 models
> hide #!9 models
> show #!10 models
> volume #10 level 0.08457
> open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1873_volume_map.mrc
Opened cryosparc_P615_J1873_volume_map.mrc as #12, grid size 360,360,360,
pixel 1.27, shown at level 0.099, step 2, values float32
> open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1876_volume_map.mrc
Opened cryosparc_P615_J1876_volume_map.mrc as #13, grid size 360,360,360,
pixel 1.27, shown at level 0.102, step 2, values float32
> volume #12 step 1
> volume #13 step 1
> volume #13 level 0.1007
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> show #!8 models
> hide #!9 models
> hide #!8 models
> show #!10 models
> hide #!10 models
> show #!9 models
> show #!8 models
> hide #!12 models
> hide #!13 models
> hide #!8 models
> hide #!9 models
> show #!10 models
> show #!11 models
> show #!13 models
> hide #!13 models
> show #!12 models
> hide #!11 models
> show #!9 models
> hide #!10 models
> hide #!9 models
> show #!13 models
> show #!10 models
> show #!11 models
> hide #!12 models
> hide #!13 models
> hide #!10 models
> hide #!11 models
> show #!9 models
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> volume #9 level 0.09286
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> show #!8 models
> show #!10 models
> hide #!9 models
> hide #!8 models
> show #!11 models
> hide #!10 models
> hide #!11 models
> show #!8 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> show #!9 models
> hide #!8 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> show #!8 models
> hide #!9 models
> show #!11 models
> hide #!10 models
> show #!10 models
> hide #!11 models
> show #!13 models
> hide #!10 models
> hide #!8 models
> show #!10 models
> close #12-13
> show #!9 models
> volume #9 level 0.09488
> show #!8 models
> volume #8 level 0.07039
> hide #!9 models
> hide #!10 models
> show #!11 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> show #!7 models
> hide #!7 models
> show #!9 models
> hide #!11 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1873_volume_map.mrc
Opened cryosparc_P615_J1873_volume_map.mrc as #12, grid size 360,360,360,
pixel 1.27, shown at level 0.099, step 2, values float32
> hide #!9 models
> open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1876_volume_map.mrc
Opened cryosparc_P615_J1876_volume_map.mrc as #13, grid size 360,360,360,
pixel 1.27, shown at level 0.102, step 2, values float32
> volume #12 level 0.06835
> volume #12 level 0.0958
> volume #13 level 0.09404
> open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1930_volume_map.mrc
Opened cryosparc_P615_J1930_volume_map.mrc as #14, grid size 360,360,360,
pixel 1.27, shown at level 0.105, step 2, values float32
> hide #!12 models
> hide #!13 models
> volume #14 level 0.08558
> volume #14 step 1
> open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1932_volume_map.mrc
Opened cryosparc_P615_J1932_volume_map.mrc as #15, grid size 360,360,360,
pixel 1.27, shown at level 0.0999, step 2, values float32
> hide #!14 models
> volume #15 level 0.07598
> open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1934_volume_map.mrc
Opened cryosparc_P615_J1934_volume_map.mrc as #16, grid size 360,360,360,
pixel 1.27, shown at level 0.0991, step 2, values float32
> hide #!15 models
> volume #16 level 0.08652
> show #!15 models
> show #!14 models
> show #!13 models
> hide #!14 models
> hide #!15 models
> hide #!16 models
> show #!14 models
> hide #!13 models
> set bgColor white
> hide #!14 models
> color #14-16 darkgrey
> show #!14 models
> show #!15 models
> show #!16 models
> hide #!15 models
> hide #!14 models
> open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
> model/20250505_P5P1-SPRY-RLD1_isolde_clean.pdb
Chain information for 20250505_P5P1-SPRY-RLD1_isolde_clean.pdb #17
---
Chain | Description
1 | No description available
A | No description available
B | No description available
> hide #!16 models
> show #!16 models
> open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
> model/20250902_composite_chain-fix.pdb
Chain information for 20250902_composite_chain-fix.pdb #18
---
Chain | Description
1 2 3 | No description available
A I K | No description available
B J L | No description available
> hide #!16 models
> show #17#!18 cartoons
> hide #17#!18 atoms
> show #!14 models
> show #!15 models
> hide #!15 models
> hide #!14 models
> show #!15 models
> show #!16 models
> hide #!15 models
> hide #!16 models
> select #18/1:3783
17 atoms, 16 bonds, 1 residue, 1 model selected
> select up
98 atoms, 97 bonds, 6 residues, 1 model selected
> select up
7957 atoms, 8046 bonds, 538 residues, 1 model selected
> select up
8105 atoms, 8193 bonds, 547 residues, 1 model selected
> select up
10637 atoms, 10758 bonds, 717 residues, 1 model selected
> select up
10868 atoms, 10992 bonds, 732 residues, 1 model selected
> select up
14205 atoms, 14374 bonds, 943 residues, 1 model selected
> select up
14286 atoms, 14455 bonds, 948 residues, 1 model selected
> select up
21639 atoms, 21880 bonds, 1408 residues, 1 model selected
> select #18/!
Expected an objects specifier or a keyword
> select #18/1
54175 atoms, 54698 bonds, 35 pseudobonds, 3516 residues, 2 models selected
> intersect dimer 1, 2 occpued, dimer 3 empty
Unknown command: intersect dimer 1, 2 occpued, dimer 3 empty
> color sel #d31340ff
> show #!16 models
> color sel #b2b2b2
> color sel #F6921E
> select up
193662 atoms, 195518 bonds, 105 pseudobonds, 12558 residues, 2 models selected
> select up
193662 atoms, 195518 bonds, 105 pseudobonds, 12558 residues, 2 models selected
> select #18/1:3561
19 atoms, 18 bonds, 1 residue, 1 model selected
> solor #18/1 #663399
Unknown command: solor #18/1 #663399
> color #18/1 #663399
> select /A:2027-2193
1304 atoms, 1335 bonds, 167 residues, 1 model selected
> select #18/1
54175 atoms, 54698 bonds, 35 pseudobonds, 3516 residues, 2 models selected
> color sel #b2b2b2
> select #18/3
54175 atoms, 54694 bonds, 35 pseudobonds, 3516 residues, 2 models selected
> color sel #6120AC
> select #18/2:3560
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #18/2
54175 atoms, 54709 bonds, 35 pseudobonds, 3516 residues, 2 models selected
> color sel #C691FF
> hide #!16 models
> hide #17 models
> select #18/A,B
10283 atoms, 10366 bonds, 669 residues, 1 model selected
> color sel #abd9e533
> color sel #abd9e533 transparency 0
> select #18/B
4397 atoms, 4428 bonds, 277 residues, 1 model selected
> color sel cyan
> color sel light blue
> color sel blue
> color sel sky blue
> color sel powder blue
> color sel steel blue
> select #18/l,K
10283 atoms, 10366 bonds, 669 residues, 1 model selected
> color sel #ffb1fd33
> color sel #ffb1fd33 transparency 0
> select #18/L:278
14 atoms, 13 bonds, 1 residue, 1 model selected
> color #18/L orchid
> color #18/I,J sea green
> select #18/1:192
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #18/I:378
11 atoms, 10 bonds, 1 residue, 1 model selected
> color #18/I light green
> select up
93 atoms, 93 bonds, 6 residues, 1 model selected
> select up
5886 atoms, 5938 bonds, 392 residues, 1 model selected
> color #18/1 #b2b2b2 transparency 80
> color #18/2 #C691FF transparency 80
> color #18/3 #6120AC transparency 80
> show #!14 models
> color zone #14 near #18 distance 8
> hide #!18 models
> color #14-16 white transparency 80
> color zone #14 near #18 distance 8
> color #14-16 white transparency 100
> color zone #14 near #18 distance 8
> color zone #14 near #18 distance 10
[Repeated 1 time(s)]
> color zone #14 near #18 distance 12
> color zone #14 near #18 distance 14
> color zone #14 near #18 distance 20
> show #!18 models
> hide #!14 models
> show sel atoms
> hide sel atoms
[Repeated 1 time(s)]
> show #18
> select #18/A,B,C
10379 atoms, 10461 bonds, 670 residues, 1 model selected
> select #18/A,H,D
6078 atoms, 6128 bonds, 394 residues, 1 model selected
> delete sel]
Missing or invalid "atoms" argument: only initial part "sel" of atom specifier
valid
> delete sel
> undo
Undo failed, probably because structures have been modified.
> close #18
> open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
> model/20250902_composite_chain-fix.pdb
Chain information for 20250902_composite_chain-fix.pdb #18
---
Chain | Description
1 2 3 | No description available
A I K | No description available
B J L | No description available
> color #18/1 #663399
> select /A:2027-2193
1304 atoms, 1335 bonds, 167 residues, 1 model selected
> select #18/1
54175 atoms, 54698 bonds, 35 pseudobonds, 3516 residues, 2 models selected
> color sel #b2b2b2
> select #18/3
54175 atoms, 54694 bonds, 35 pseudobonds, 3516 residues, 2 models selected
> color sel #6120AC
> select #18/2
54175 atoms, 54709 bonds, 35 pseudobonds, 3516 residues, 2 models selected
> color sel #C691FF
> select #18/A,B
10283 atoms, 10366 bonds, 669 residues, 1 model selected
> color sel #abd9e533
> color sel #abd9e533 transparency 0
> select #18/B
4397 atoms, 4428 bonds, 277 residues, 1 model selected
> color sel cyan
> color sel light blue
> color sel blue
> color sel sky blue
> color sel powder blue
> color sel steel blue
> select #18/l,K
10283 atoms, 10366 bonds, 669 residues, 1 model selected
> color sel #ffb1fd33
> color sel #ffb1fd33 transparency 0
> color #18/L orchid
> color #18/I,J sea green
> color #18/I light green
> color #18/1 #b2b2b2 transparency 80
> color #18/2 #C691FF transparency 80
> color #18/3 #6120AC transparency 80
> select #18/C,D,H
288 atoms, 285 bonds, 3 residues, 1 model selected
> delete sel
> show #!14 models
> show #!15 models
> hide #!14 models
> hide #!15 models
> show #!14 models
> hide #!14 models
> show #!15 models
> hide #!18 models
> show #!18 models
> color #14-16 white transparecny 80
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #14-16 white transparency 80
> color #14-16 white transparency 100
> color #14-16 white transparency 80
> show #!14 models
> hide #!15 models
> color zone #14 near #18 distance 20
> hide #!18 models
> show #!15 models
> hide #!14 models
> show #!18 models
> color zone #14 near #18 & ~/I,J distance 20
> color zone #14 near #18 distance 20
> color zone #15 near #18 & ~/I,J distance 20
> show #!16 models
> hide #!15 models
> color zone #15 near #18 & ~/K,L distance 20
> color #14-16 white transparency 80
> color zone #14 near #18 distance 20
> color zone #15 near #18 & ~/I,J distance 20
> color zone #16 near #18 & ~/K,L distance 20
> hide #!18 models
> color #16 white transparency 80
> color zone #16 near #18 & ~/I,J,K,L distance 20
> show #!15 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!15 models
> hide #!16 models
> hide #!14 models
> show #!14 models
> open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1936_volume_map.mrc
Opened cryosparc_P615_J1936_volume_map.mrc as #19, grid size 360,360,360,
pixel 1.27, shown at level 0.104, step 2, values float32
> hide #!14 models
> show #!14 models
> volume #19 step 1
> volume #16 step 1
> volume #15 step 1
> volume #13 step 1
> volume #19 level 0.08332
> hide #!14 models
> show #!18 models
> color zone #19 near #18 & ~/K,L distance 20
> hide #!19 models
> show #!19 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> volume #19 level 0.1091
> volume #19 level 0.0865
> color #19 white transparency 80
> color zone #19 near #18 & ~/K,L distance 20
> color #19 white transparency 100
> color zone #19 near #18 & ~/K,L distance 20
> graphics silhouettes true width 4
> graphics silhouettes true width 2
> volume #19 level 0.1
> volume #16 level 0.1
> show #!16 models
> hide #!19 models
> show #!15 models
> hide #!16 models
> volume #15 level 0.1
> volume #14 level 0.1
> show #!14 models
> hide #!15 models
> volume #14 level 0.09
> show #!15 models
> hide #!14 models
> volume #15 level 0.9
> volume #15 level 0.09
> show #!16 models
> hide #!15 models
> volume #16 level 0.09
> volume #19 level 0.09
> show #!19 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!16 models
> show #!16 models
> hide #!19 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> show #!19 models
> show #!18 models
> hide #!19 models
> hide #!16 models
> hide #!15 models
> show #!18 cartoons
> hide #!18 atoms
> color #18/A ABAA00
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #18/A #ABAA00
> color #18/B #ABAA00
> color #18/A #363600
> color #18/K 005A4A
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #18/K #005A4A
> color #18/L #2CC9A6
> color #18/I #1F2A44
> color #18/J #5B7DBB
> color #14-16,19 white transparency 80
> color zone #19 near #18 & ~/K,L distance 20
> color zone #16 near #18 & ~/I,J,K,L distance 20
> color zone #15 near #18 & ~/I,J distance 20
> color zone #14 near #18 distance 20
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!18 models
> show #!16 models
> hide #!19 models
> show #!15 models
> hide #!16 models
> show #!14 models
> hide #!15 models
> show #!15 models
> hide #!14 models
> show #!16 models
> hide #!15 models
> show #!19 models
> hide #!19 models
> show #!15 models
> hide #!15 models
> hide #!16 models
> show #!14 models
> view name bottom_overview
> close #3#1-2,4-7
> open
> /Users/lorenz.grundmann/Downloads/cryosparc_P615_J772_011_volume_map.mrc
Opened cryosparc_P615_J772_011_volume_map.mrc as #1, grid size 360,360,360,
pixel 1.27, shown at level 0.099, step 2, values float32
> hide #!14 models
> volume #1 step 1
> color #1 darkgrey
> open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J528_mask.mrc
Opened cryosparc_P615_J528_mask.mrc as #2, grid size 240,240,240, pixel 1.9,
shown at level 5e-05, step 1, values float32
> volume #2 level 0.3808
> open "/Users/lorenz.grundmann/Downloads/cryosparc_P615_J526_mask (1).mrc"
Opened cryosparc_P615_J526_mask (1).mrc as #3, grid size 240,240,240, pixel
1.9, shown at level 5e-05, step 1, values float32
> open "/Users/lorenz.grundmann/Downloads/cryosparc_P615_J453_mask (1).mrc"
Opened cryosparc_P615_J453_mask (1).mrc as #4, grid size 360,360,360, pixel
1.27, shown at level 5e-05, step 2, values float32
> hide #!2 models
> hide #!3 models
> hide #!4 models
> show #!18 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> show #!1 models
> hide #!4 models
> show #!16 models
> hide #!16 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> volume #2 level 0.5
> volume #3 level 0.5
> volume #4 level 0.5
> color #4 #707000 transparency 80
> show #!2 models
> hide #!4 models
> color #2 #168E78 transparency 80
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!2 models
> color #3 #168E78 transparency 80
> color #2 #3D5480 transparency 80
> show #!2 models
> show #!4 models
> hide #!18 models
> show #!1 models
> view name side_overview
> turn x 90
[Repeated 3 time(s)]
> turn x -90
> turn z -45
> turn z -120
[Repeated 2 time(s)]
> turn z 120
> view name bottom_overview
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> cd "/Users/lorenz.grundmann/VBC Dropbox/Group Folder
> Haselbach/Projects/HERC1/Lorenz/P615_ZH027_ZH034-xlinked_P5P1_occupancy"
Current working directory is: /Users/lorenz.grundmann/VBC Dropbox/Group Folder
Haselbach/Projects/HERC1/Lorenz/P615_ZH027_ZH034-xlinked_P5P1_occupancy
> save J772_consensus_bottom.png width 3000 height 3000 supersample 3
> transparentBackground true
> view list
Named views: bottom_overview, side_overview
> view side_overview
> save J772_consensus_side.png width 3000 height 3000 supersample 3
> transparentBackground true
> graphics silhouettes true width 4
> view bottom_overview
> save J772_consensus_bottom.png width 3000 height 3000 supersample 3
> transparentBackground true
> view side_overview
> save J772_consensus_side.png width 3000 height 3000 supersample 3
> transparentBackground true
> lighting full
> lighting soft
> save J772_consensus_side.png width 3000 height 3000 supersample 3
> transparentBackground true
> view bottom_overview
> save J772_consensus_bottom.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> show #!14 models
> show #!2 models
> hide #!2 models
> hide all models
> shoe #14 model
Unknown command: shoe #14 model
> view bottom overview
Expected an objects specifier or a view name or a keyword
> view bottom_overview
> show #14 models
> save J1930_arm-1-2-3_occupied_bottom.png width 3000 height 3000 supersample
> 3 transparentBackground true
> show #!15 models
> hide #!14 models
> show #!14 models
> hide #!15 models
> hide #14 models
> show #15 models
> save J1932_arm-1-2_occupied_bottom.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #15 models
> show #16 models
> save J1934_arm-1_occupied_bottom.png width 3000 height 3000 supersample 3
> transparentBackground true
> show #!19 models
> hide #!19 models
> hide #16 models
> show #19 models
> save J1934_arm-1-3_occupied_bottom.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide all models
> view side_overview
> show #14 models
> save J1930_arm-1-2-3_occupied_side.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #14 models
> show #15 models
> save J1932_arm-1-2_occupied_side.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #15 models
> show #16 models
> save J1934_arm-1_occupied_side.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #16 models
> show #19 models
> save J1934_arm-1-3_occupied_side.png width 3000 height 3000 supersample 3
> transparentBackground true
> save occupancy_analysis.cxs includeMaps true
> hide #!19 models
> show #!16 models
> hide #!16 models
> show #!19 models
> color #4 #707000 transparency 20
> color #2 #168E78 transparency 20
> color #2 #3D5480 transparency 20
> color #18/3 #6120AC transparency 20
> color #18/1 #b2b2b2 transparency 20
> color #18/2 #C691FF transparency 20
> color #18/A #ABAA00
> color #18/B #ABAA00
> color #18/A #363600
> color #18/K #005A4A
> color #18/L #2CC9A6
> color #18/I #1F2A44
> color #18/J #5B7DBB
> color zone #14 near #18 distance 20
> color #14-16,19 white transparency 20
> color zone #19 near #18 & ~/K,L distance 20
> color zone #16 near #18 & ~/I,J,K,L distance 20
> color zone #15 near #18 & ~/I,J distance 20
> color zone #14 near #18 distance 20
> show #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #1-4 models
> hide #!19 models
> hide all models
> view bottom_overview
> show #1-4 models
> save J772_consensus_bottom.png width 3000 height 3000 supersample 3
> transparentBackground true
> show #14 models
> save J1930_arm-1-2-3_occupied_bottom.png width 3000 height 3000 supersample
> 3 transparentBackground true
> hide #14 models
> show #15 models
> save J1932_arm-1-2_occupied_bottom.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #15 models
> show #16 models
> save J1934_arm-1_occupied_bottom.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #16 models
> show #19 models
> save J1934_arm-1-3_occupied_bottom.png width 3000 height 3000 supersample 3
> transparentBackground true
> Make the figures
Unknown command: Make the figures
> hide all models
> view bottom_overview
> show #1-4 models
> hide all models
> save J772_consensus_bottom.png width 3000 height 3000 supersample 3
> transparentBackground true
> show #14 models
> save J1930_arm-1-2-3_occupied_bottom.png width 3000 height 3000 supersample
> 3 transparentBackground true
> hide #14 models
> show #15 models
> save J1932_arm-1-2_occupied_bottom.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #15 models
> show #16 models
> save J1934_arm-1_occupied_bottom.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #16 models
> show #19 models
> save J1934_arm-1-3_occupied_bottom.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide all models
> view bottom_overview
> show #1-4 models
> save J772_consensus_bottom.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide all models
> color #4 #707000 transparency 50
> color #2 #168E78 transparency 50
> color #2 #3D5480 transparency 50
> hide all models
> view bottom_overview
> show #1-4 models
> save J772_consensus_bottom.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide all models
> show #14 models
> save J1930_arm-1-2-3_occupied_bottom.png width 3000 height 3000 supersample
> 3 transparentBackground true
> hide #14 models
> show #15 models
> save J1932_arm-1-2_occupied_bottom.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #15 models
> show #16 models
> save J1934_arm-1_occupied_bottom.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #16 models
> show #19 models
> save J1934_arm-1-3_occupied_bottom.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide all models
> view side_overview
> show #1-4 models
> save J772_consensus_side.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide all models
> show #14 models
> save J1930_arm-1-2-3_occupied_side.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #14 models
> show #15 models
> save J1932_arm-1-2_occupied_side.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #15 models
> show #16 models
> save J1934_arm-1_occupied_side.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #16 models
> show #19 models
> save J1934_arm-1-3_occupied_side.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #!19 models
> show #!4 models
> hide #!4 models
> show #8 models
> show #8-16 models
> hide #!14-16 target m
> hide #!10-13 target m
> hide #!9 models
> hide #!8 models
> show #!9 models
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> volume #8 level 0.0949
> volume #9 level 0.0846
> volume #8 level 0.0846
> volume #11 level 0.0846
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> show #!12 models
> hide #!11 models
> hide #!8 models
> hide #!9 models
> show #!13 models
> hide #!12 models
> show #!11 models
> hide #!11 models
> close #12-13
> open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1711_volume_map.mrc
Opened cryosparc_P615_J1711_volume_map.mrc as #5, grid size 360,360,360, pixel
1.27, shown at level 0.0987, step 2, values float32
> open /Users/lorenz.grundmann/Downloads/cryosparc_P615_J1714_volume_map.mrc
Opened cryosparc_P615_J1714_volume_map.mrc as #6, grid size 360,360,360, pixel
1.27, shown at level 0.099, step 2, values float32
> hide #!6 models
> show #!6 models
> volume #5 step 1
> volume #6 step 1
> volume #5 level 0.08297
> show #!18 models
> hide #!5 models
> show #!5 models
> color #5 darkgrey
> color #5 near #18/A,B dist 6
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color zone #5 near #18/A,B distance 6
> ui tool show "Side View"
> save test.png width 3000 height 3000 supersample 3 transparentBackground
> true
[Repeated 1 time(s)]
> hide #!18 models
> show #!6 models
> hide #!5 models
> color #6 darkgrey
> color zone #6 near #18/A,B distance 6
> save J17114_class-3D_P5P1-dimer-1-reconstruct.png width 3000 height 3000
> supersample 3 transparentBackground true
> save J1714_class-3D_P5P1-dimer-1-reconstruct.png width 3000 height 3000
> supersample 3 transparentBackground true
> show #!5 models
> hide #!6 models
> save J1711_class-3D_P5P1-dimer-1-reconstruct.png width 3000 height 3000
> supersample 3 transparentBackground true
> view name diemr_1_close
> view list
Named views: bottom_overview, diemr_1_close, side_overview
> view side_overview
> show #!1 models
> hide #!5 models
> view #1 m
Expected an integer >= 1 or a keyword
> show #1 models
> show #!4 models
> show #4 models
> save J772_P5P1-dimer1-mask.png height 3000 width 3000 supersample 3
> transparentBackground true
> turn y 120
> show #!3 models
> hide #!4 models
> show #3 models
> show #2
> hide #!2 models
> show #!2 models
> hide #!3 models
> save J772_P5P1-dimer3-mask.png height 3000 width 3000 supersample 3
> transparentBackground true
> turn y 120
> show #!3 models
> hide #!2 models
> show #!2 models
> turn y 120
[Repeated 1 time(s)]
> hide #!3 models
> save J772_P5P1-dimer3-mask.png height 3000 width 3000 supersample 3
> transparentBackground true
> turn y 120
> show #!3 models
> hide #!2 models
> save J772_P5P1-dimer2-mask.png height 3000 width 3000 supersample 3
> transparentBackground true
> color #3 #168e781b models
> color #3 #168e7800 models
> color #3 #168e7880 models
> save J772_P5P1-dimer2-mask.png height 3000 width 3000 supersample 3
> transparentBackground true
> graphics silhouettes true width 8
> save J772_P5P1-dimer2-mask.png height 3000 width 3000 supersample 3
> transparentBackground true
> graphics silhouettes true width 16
> save J772_P5P1-dimer2-mask.png height 3000 width 3000 supersample 3
> transparentBackground true
> graphics silhouettes true width 32
> save J772_P5P1-dimer2-mask.png height 3000 width 3000 supersample 3
> transparentBackground true
> view list
Named views: bottom_overview, diemr_1_close, side_overview
> side_overview_P5P1_dimer_2
Unknown command: side_overview_P5P1_dimer_2
> view name side_overview_P5P1_dimer_2
> turn y 12
[Repeated 1 time(s)]
> turn y -12
[Repeated 1 time(s)]
> turn y 120
> hide #!3 models
> show #!4 models
> save J772_P5P1-dimer1-mask.png height 3000 width 3000 supersample 3
> transparentBackground true
> show #!3 models
> hide #!4 models
> show #!2 models
> hide #!3 models
> show #!4 models
> hide #!2 models
> view list
Named views: bottom_overview, diemr_1_close, side_overview,
side_overview_P5P1_dimer_2
> view side_overview
> save J772_P5P1-dimer1-mask.png height 3000 width 3000 supersample 3
> transparentBackground true
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!4 models
> undo
> redo
> view side_overview
> hide #!4 models
> turn y 120
> view name side_overview_P5P1_dimer_3
> save J772_P5P1-dimer3-mask.png height 3000 width 3000 supersample 3
> transparentBackground true
> graphics silhouettes true width 4
> hide #!2 models
> hide #!1 models
> show #!14 models
> show #!15 models
> hide #!14 models
> show #!16 models
> hide #!15 models
> show #!19 models
> hide #!16 models
> show #!15 models
> hide #!19 models
> show #!19 models
> hide #!15 models
> pwd
Current working directory is: /Users/lorenz.grundmann/VBC Dropbox/Group Folder
Haselbach/Projects/HERC1/Lorenz/P615_ZH027_ZH034-xlinked_P5P1_occupancy
> view list
Named views: bottom_overview, diemr_1_close, side_overview,
side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view diemr_1_close
> turn y 120
> view side_overview_P5P1_dimer_2
> view diemr_1_close
> view name dimer_1_close
> view delete diemer_1_close
> view list
Named views: bottom_overview, diemr_1_close, dimer_1_close, side_overview,
side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view dimer_1_close
> view dimer_2 close
Expected an objects specifier or a view name or a keyword
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> view list
Named views: bottom_overview, diemr_1_close, dimer_1_close, side_overview,
side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view side_overview_P5P1_dimer_3
> hide #!19 models
> show #!5 models
> show #!6 models
> hide #!5 models
> show #!8 models
> hide #!6 models
> show #!9 models
> hide #!8 models
> show #!10 models
> hide #!9 models
> show #!11 models
> hide #!10 models
> show #!10 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> show #!18 models
> hide #!10 models
> hide #!11 models
> show #!11 models
> show #!10 models
> hide #!11 models
> color #10,11 darkgrey
> show #!11 models
> hide #!10 models
> hide #!11 models
> color zone #11 near #18/J,I distance 6
> show #!11 models
> show #!10 models
> hide #!11 models
> show #!11 models
> hide #!10 models
> color #10,11 darkgrey
> color zone #11 near #18/J,I distance 4
> hide #!18 models
> show #!18 models
> hide #!18 models
> save test.png width 3000 height 3000 supersample 3 transparentBackground
> true
> view name dimer_3_close
> save J1846_class-3D_P5P1-dimer-3-reconstruct.png width 3000 height 3000
> supersample 3 transparentBackground true
> show #!10 models
> hide #!11 models
> show #!11 models
> hide #!10 models
> save J1846_class-3D_P5P1-dimer-3-reconstruct.png width 3000 height 3000
> supersample 3 transparentBackground true
> show #!10 models
> hide #!11 models
> save J1843_class-3D_P5P1-dimer-3-reconstruct.png width 3000 height 3000
> supersample 3 transparentBackground true
> hide #!10 models
> show #!8 models
> show #!9 models
> view list
Named views: bottom_overview, diemr_1_close, dimer_1_close, dimer_3_close,
side_overview, side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view side_overview_P5P1_dimer_2
> hide #!9 models
> show #!9 models
> hide #!8 models
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> show #!8 models
> color #8,9 darkgrey
> show #!18 models
> hide #!8 models
> color zone #10 near #18/K,L distance 6
> show #!10 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!10 models
> show #!9 models
> hide #!8 models
> show #!8 models
> color #10,11 darkgrey
> color zone #11 near #18/J,I distance 4
> hide #!9 models
> color zone #8 near #18/K,L distance 6
> hide #!18 models
> show #!9 models
> hide #!8 models
> show #!8 models
> save test.png width 3000 height 3000 supersample 3 transparentBackground
> true
> view name dimer_2_close
> hide #!9 models
> show #!9 models
> hide #!8 models
> save J1786_class-3D_P5P1-dimer-2-reconstruct.png width 3000 height 3000
> supersample 3 transparentBackground true
> show #!8 models
> hide #!9 models
> save J1783_class-3D_P5P1-dimer-2-reconstruct.png width 3000 height 3000
> supersample 3 transparentBackground true
> hide #!8 models
> show #!10 models
> show #!14 models
> hide #!10 models
> show #!15 models
> hide #!14 models
> hide #!15 models
> show #!16 models
> show #!14 models
> hide #!16 models
> show #!16 models
> hide #!14 models
> show #!19 models
> show #17 models
> hide #!16 models
> hide #17 models
> save analysis-cxs i t
Cannot determine format for 'analysis-cxs'
> save analysis.cxs includeMaps true
——— End of log from Mon Jan 19 11:45:42 2026 ———
opened ChimeraX session
> open
> /Users/lorenz.grundmann/Downloads/fold_herc2_1_1550_3mer/fold_herc2_1_1550_3mer_model_0.cif
Chain information for fold_herc2_1_1550_3mer_model_0.cif #7
---
Chain | Description
A B C | .
Computing secondary structure
> hide #7 models
> hide #!19 models
> show #!19 models
> open
> /Users/lorenz.grundmann/Downloads/fold_herc2_1_1550_3mer/fold_herc2_1_1550_3mer_model_0.cif
Chain information for fold_herc2_1_1550_3mer_model_0.cif #12
---
Chain | Description
A B C | .
Computing secondary structure
> hide #!19 models
> view #12 clip false
> color bychain
> open /Users/lorenz.grundmann/Downloads/fold_herc2/fold_herc2_model_0.cif
Chain information for fold_herc2_model_0.cif #13
---
Chain | Description
A | .
Computing secondary structure
> matchmaker #13 to #12/A
Computing secondary structure
[Repeated 1 time(s)] 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 fold_herc2_1_1550_3mer_model_0.cif, chain A (#12) with
fold_herc2_model_0.cif, chain A (#13), sequence alignment score = 7500.8
RMSD between 485 pruned atom pairs is 1.091 angstroms; (across all 1500 pairs:
22.343)
> rainbow #13
> open
> /Users/lorenz.grundmann/Downloads/fold_19s_base_paaf1/fold_19s_base_paaf1_job_request.json
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open
/Users/lorenz.grundmann/Downloads/fold_19s_base_paaf1/fold_19s_base_paaf1_job_request.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> open
> /Users/lorenz.grundmann/Downloads/fold_19s_base_paaf1/fold_19s_base_paaf1_model_0.cif
Chain information for fold_19s_base_paaf1_model_0.cif #20
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
G | .
H | .
I | .
J | .
K | .
L | .
> hide #12 models
> hide #13 models
> show #20 cartoons
Computing secondary structure
> hide #20 atoms
> hide #20 models
> show #20 models
> open
> /Users/lorenz.grundmann/Downloads/fold_19s_base_paaf1/fold_19s_base_paaf1_full_data_0.json
Opened AlphaFold PAE with values for 4971 residues and atoms
> color #20/K:856/L lime
> open "/Users/lorenz.grundmann/Downloads/cryosparc_P561_J448_009_volume_map
> (1).mrc"
Opened cryosparc_P561_J448_009_volume_map (1).mrc as #21, grid size
360,360,360, pixel 1.27, shown at level 0.0807, step 2, values float32
> hide #20 models
> view #21 clip false
> open
> /Users/lorenz.grundmann/Downloads/cryosparc_P561_J254_009_volume_map.mrc
Opened cryosparc_P561_J254_009_volume_map.mrc as #22, grid size 360,360,360,
pixel 1.27, shown at level 0.0788, step 2, values float32
> hide #!21 models
> volume #22 level 0.05311
> volume #22 step 1
> volume #22 level 0.08379
> show #!21 models
> hide #!22 models
> volume #21 step 1
> volume #21 level 0.1209
> open
> /Volumes/Herc/20241024_ZH027_Hek_Herc1_PSMC5_PAAF1/relion/J448/Refine3D/local_sampling_lp-12/run_class001.mrc
Opened run_class001.mrc as #23, grid size 360,360,360, pixel 1.27, shown at
level 0.00236, step 2, values float32
> volume #23 level 0.003573
> volume #23 step 1
> hide #!21 models
> volume #23 level 0.003573
> volume #23 level 0.004357
> color #28/1:372-734 light sky blue
> color #28/1:3420-3820 #350CED
> color #28/1:3996-4366 #90CED6
> color #28/1:4447-4840 #d31340ff
> color #28/1:2315-2379 palegreen
> color #28/1:1384-1399 #009193ff
> color #28/1:2747-2799 lime
> color #28/1:2975-3055 #EF6B11
> color #28/1:2075-2186 #F4EB45
> color #28/1:3297-3329 #CE3674
> close
> windowsize 1200 1200
> open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
> model/20260203_franekenmodel_new.pdb
Chain information for 20260203_franekenmodel_new.pdb #1
---
Chain | Description
1 | No description available
2 3 | No description available
A C E | No description available
B D F | No description available
> open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
> model/20260203_frankenmap.mrc
Opened 20260203_frankenmap.mrc as #2, grid size 360,360,360, pixel 1.27, shown
at level 0.14, step 2, values float32
> volume #2 step 1
> fitmap #1 inMap #2
Fit molecule 20260203_franekenmodel_new.pdb (#1) to map
20260203_frankenmap.mrc (#2) using 193662 atoms
average map value = 0.1852, steps = 124
shifted from previous position = 2.36
rotated from previous position = 2.79 degrees
atoms outside contour = 111278, contour level = 0.1401
Position of 20260203_franekenmodel_new.pdb (#1) relative to
20260203_frankenmap.mrc (#2) coordinates:
Matrix rotation and translation
0.99898431 -0.02740180 0.03577001 0.08643429
0.02805832 0.99944452 -0.01798280 -3.96522601
-0.03525738 0.01896818 0.99919824 4.42656013
Axis 0.37938688 0.72925970 0.56942592
Axis point 131.06536616 0.00000000 -2.28277335
Rotation angle (degrees) 2.79130992
Shift along axis -0.33828942
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show cartoons
> hide atoms
> show #!2 models
> fitmap #1 inMap #2
Fit molecule 20260203_franekenmodel_new.pdb (#1) to map
20260203_frankenmap.mrc (#2) using 193662 atoms
average map value = 0.1852, steps = 64
shifted from previous position = 0.019
rotated from previous position = 0.00619 degrees
atoms outside contour = 111364, contour level = 0.1401
Position of 20260203_franekenmodel_new.pdb (#1) relative to
20260203_frankenmap.mrc (#2) coordinates:
Matrix rotation and translation
0.99898711 -0.02743147 0.03566887 0.12837483
0.02808688 0.99944331 -0.01800537 -3.96190269
-0.03515510 0.01898896 0.99920145 4.41043263
Axis 0.38021682 0.72790771 0.57060104
Axis point 130.70040370 0.00000000 -3.28257276
Rotation angle (degrees) 2.78848325
Shift along axis -0.31849179
> close #1
> open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
> model/20260203_franekenmodel_new.pdb
Summary of feedback from opening
/Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
model/20260203_franekenmodel_new.pdb
---
warnings | Start residue of secondary structure not found: HELIX 114 114 ILE F 298 ILE F 300 1 3
Start residue of secondary structure not found: HELIX 115 115 SER F 303 LEU F
305 1 3
Start residue of secondary structure not found: HELIX 116 116 GLU F 322 HIS F
332 1 11
Start residue of secondary structure not found: HELIX 117 117 SER F 333 LYS F
335 1 3
Start residue of secondary structure not found: HELIX 118 118 LEU F 344 GLU F
349 1 6
756 messages similar to the above omitted
Ignored bad PDB record found on line 47792
RG F 297 190.126 173.141 191.732 1.00 53.47 N
Chain information for 20260203_franekenmodel_new.pdb
---
Chain | Description
1.1/1 | No description available
1.1/2 | No description available
1.1/3 | No description available
1.1/A 1.1/E | No description available
1.1/B 1.1/F | No description available
1.2/F | No description available
> close #1
> close #2
> open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
> model/20260203_franekenmodel_new.pdb
Summary of feedback from opening
/Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
model/20260203_franekenmodel_new.pdb
---
warnings | End residue of secondary structure not found: HELIX 305 305 VAL 3 2557 ARG 3 2573 1 17
Start residue of secondary structure not found: HELIX 306 306 VAL 3 3190 LEU 3
3197 1 8
Start residue of secondary structure not found: HELIX 307 307 SER 3 3203 LEU 3
3210 1 8
Start residue of secondary structure not found: HELIX 308 308 ILE 3 3218 ALA 3
3229 1 12
Start residue of secondary structure not found: HELIX 309 309 LEU 3 3263 ALA 3
3274 1 12
Start residue of secondary structure not found: HELIX 310 310 PRO 3 3278 THR 3
3297 1 20
412 messages similar to the above omitted
Ignored bad PDB record found on line 112037
566 293.184 107.305 203.880 1.00 92.87 H
Chain information for 20260203_franekenmodel_new.pdb
---
Chain | Description
1.1/1 | No description available
1.1/2 | No description available
1.1/3 | No description available
1.2/3 | No description available
1.1/A 1.1/C 1.1/E | No description available
1.1/B 1.1/D 1.1/F | No description available
Computing secondary structure
> hide #!1.2 models
> hide #!1.1 models
> close #1
> open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
> model/20260203_franekenmodel_new.pdb
Chain information for 20260203_franekenmodel_new.pdb #1
---
Chain | Description
1 | No description available
2 3 | No description available
A C E | No description available
B D F | No description available
> open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
> model/20260203_frankenmap.mrc
Opened 20260203_frankenmap.mrc as #2, grid size 360,360,360, pixel 1.27, shown
at level 0.14, step 2, values float32
> fitmap #1 inMap #2
Fit molecule 20260203_franekenmodel_new.pdb (#1) to map
20260203_frankenmap.mrc (#2) using 193662 atoms
average map value = 0.1852, steps = 124
shifted from previous position = 2.36
rotated from previous position = 2.79 degrees
atoms outside contour = 101671, contour level = 0.1401
Position of 20260203_franekenmodel_new.pdb (#1) relative to
20260203_frankenmap.mrc (#2) coordinates:
Matrix rotation and translation
0.99898431 -0.02740180 0.03577001 0.08643429
0.02805832 0.99944452 -0.01798280 -3.96522601
-0.03525738 0.01896818 0.99919824 4.42656013
Axis 0.37938688 0.72925970 0.56942592
Axis point 131.06536616 0.00000000 -2.28277335
Rotation angle (degrees) 2.79130992
Shift along axis -0.33828942
> volume #2 level 0.05999
> volume #2 step 1
> close
> open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
> model/20260203_frankemnmap.mrc
Opened 20260203_frankemnmap.mrc as #1, grid size 360,360,360, pixel 1.27,
shown at level 0.141, step 2, values float32
> open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
> model/20260203_frankemnmodel.pdb
Summary of feedback from opening
/Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
model/20260203_frankemnmodel.pdb
---
warnings | End residue of secondary structure not found: HELIX 142 142 ARG 3 4680 LEU 3 4692 1 13
Start residue of secondary structure not found: HELIX 143 143 ASP 3 4696 GLY 3
4705 1 10
Start residue of secondary structure not found: HELIX 144 144 MET 3 4706 TRP 3
4708 1 3
Start residue of secondary structure not found: HELIX 145 145 VAL 3 4712 LEU 3
4717 1 6
Start residue of secondary structure not found: HELIX 146 146 ALA 3 4720 CYS 3
4728 1 9
Start residue of secondary structure not found: HELIX 147 147 VAL 3 4735 LYS 3
4740 1 6
724 messages similar to the above omitted
Ignored bad PDB record found on line 55477
GLU 34689 256.307 357.171 212.206 1.00 65.82 C
Chain information for 20260203_frankemnmodel.pdb
---
Chain | Description
2.1/1 | No description available
2.1/3 | No description available
2.2/3 | No description available
2.1/A | No description available
2.1/B | No description available
2.1/E 2.1/F 2.1/G | No description available
> volume #1 step 1
> open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
> model/20260203_frankemnmodel.pdb
Chain information for 20260203_frankemnmodel.pdb #3
---
Chain | Description
1 8 9 | No description available
2 5 7 | No description available
3 4 6 | No description available
A I K | No description available
B J L | No description available
E F G | No description available
> hide #!1 models
> show #!1 models
> hide #!2 models
Cell requested for row 1 is out of bounds for table with 5 rows! Resizing
table model.
> close #2
> volume #1 level 0.008212
> hide atoms
> show cartoons
> volume #1 level 0.05603
> volume #1 level 0.1278
> volume #1 color #b2b2b281
> volume #1 level 0.2712
> open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
> model/20260203_frankemnmodel.pdb
Chain information for 20260203_frankemnmodel.pdb #2
---
Chain | Description
1 8 9 | No description available
2 5 7 | No description available
3 4 6 | No description available
A I K | No description available
B J L | No description available
E F G | No description available
> open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
> model/20260203_frankemnmap.mrc
Opened 20260203_frankemnmap.mrc as #4, grid size 360,360,360, pixel 1.27,
shown at level 0.141, step 2, values float32
> hide #!2 models
> hide #!1 models
> close #1-4
> open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
> model/20260203_frankemnmodel.pdb
Chain information for 20260203_frankemnmodel.pdb #1
---
Chain | Description
1 8 9 | No description available
2 5 7 | No description available
3 4 6 | No description available
A I K | No description available
B J L | No description available
E F G | No description available
> open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
> model/20260203_frankemnmap.mrc
Opened 20260203_frankemnmap.mrc as #2, grid size 360,360,360, pixel 1.27,
shown at level 0.141, step 2, values float32
> volume #2 step 1
> volume #2 level 0.05606
> hide #!1 models
> show #!1 models
> hide H
> style stick
Changed 192903 atom styles
> hide atoms
> show cartoons
> hide #!2 models
> hide #!1 models
> show #!1 models
> close #1
> open /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/frankenmap-
> model/20260203_frankemnmodel.pdb
Chain information for 20260203_frankemnmodel.pdb #1
---
Chain | Description
1 | No description available
2 3 | No description available
A C E | No description available
B D F | No description available
> show #!2 models
> hide atoms
> show cartoons
> hide #!2 models
> color #1/1 #BBBDBF
> color #1/2 #C691FF
> color #1/2 #6120AC
> color #1/3 #6120AC
> color #1/2 #C691FF
> color #1/1,-3:372-734 light sky blue
> color #1/1,-3:3420-3820 #350CED
> color #1/1,-3:3996-4366 #90CED6
> color #1/1,-3:4447-4840 #d31340ff
> color #1/1,-3:2315-2379 palegreen
> color #1/1,-3:1384-1399 #009193ff
> color #1/1,-3:2747-2799 lime
> color #1/1,-3:2975-3055 #EF6B11
> color #1/1,-3:2030-2190 #F4EB45
> color #1/1,-3:3297-3329 #CE3674
> color #1/1-3:372-734 light sky blue
> color #1/1-3:3420-3820 #350CED
> color #1/1-3:3996-4366 #90CED6
> color #1/1-3:4447-4840 #d31340ff
> color #1/1-3:2315-2379 palegreen
> color #1/1-3:1384-1399 #009193ff
> color #1/1-3:2747-2799 lime
> color #1/1-3:2975-3055 #EF6B11
> color #1/1-3:2030-2190 #F4EB45
> color #1/1-3:3297-3329 #CE3674
> color #1/A #363600
> color #1/B #ABAA00
> color #1/C #005A4A
> color #1/D #2CC9A6
> color #1/E #1F2A44
> color #1/F #5B7DBB
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> combine #1
> hide #!1 models
> show #!2 models
> volume #2 level 0.07655
> color zone #2 near #1 r 6
Expected a keyword
> color zone #2 near #1 distance 6
> hide #!2 models
> show #!2 models
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting soft
> hide #!2 models
> color #1/1 #BBBDBF
> color #1/2 #C691FF
> color #1/3 #6120AC
> color zone #2 near #1 distance 6
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!2 models
> color #1/a-c dark grey
> color zone #2 near #1 distance 6
> show #!2 models
> hide #!3 models
> hide #!2 models
> open
> /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/PSMC5-PAAF1-interface/20260114_P5P1_new-
> fit.cif
Summary of feedback from opening
/Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/PSMC5-PAAF1-interface/20260114_P5P1_new-
fit.cif
---
warnings | Unknown polymer entity '1' on line 166
Unknown polymer entity '2' on line 6052
Unknown polymer entity '3' on line 9979
Unknown polymer entity '4' on line 15357
Atom H is not in the residue template for LEU /B:137
Atom H is not in the residue template for GLU /C:370
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for 20260114_P5P1_new-fit.cif #4
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> open
> /Volumes/Herc/20250320-ZH027-ZH034-Xlink-2nd/model_building/PSMC5-PAAF1-interface/cryosparc_P615_J1927_014_volume_map.mrc
Opened cryosparc_P615_J1927_014_volume_map.mrc as #5, grid size 360,360,360,
pixel 1.27, shown at level 0.0844, step 2, values float32
> hide #!5 models
> hide #!4 models
> show #!4 models
> dssp #4
Computing secondary structure
> select #4/C,D 1
Expected a keyword
> changechains #4/C,D 1
Chain IDs of 530 residues changed
> windowsize 1100 1100
> color #4/1 #BBBDBF
> color #4/A #363600
> color #4/B #ABAA00
> show #!2 models
> hide #!2 models
> show #!5 models
> volume #5 step 1
> volume #5 level 0.2004
> color #5 #ffffb282 models
> color #4/1-3:372-734 light sky blue
> color #4/1-3:3420-3820 #350CED
> color #4/1-3:3996-4366 #90CED6
> color #4/1-3:4447-4840 #d31340ff
> color #4/1-3:2315-2379 palegreen
> color #4/1-3:1384-1399 #009193ff
> color #4/1-3:2747-2799 lime
> color #4/1-3:2975-3055 #EF6B11
> color #4/1-3:2030-2190 #F4EB45
> color #4/1-3:3297-3329 #CE3674
> color #5 near #4 tr 50
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #5 near #4
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color zone #5 near #4 trans 50
Expected a keyword
> color zone #5 near #4
> color zone #5 near #4 r 6
Expected a keyword
> color zone #5 near #4 distance 6
> transparency #5 50
> lighting soft
> color #4/1-3:372-734 light sky blue
> color #4/1-3:3420-3820 #350CED
> color #4/1-3:3996-4366 #90CED6
> color #4/1-3:4447-4840 #d31340ff
> color #4/1-3:2315-2379 palegreen
> color #4/1-3:1384-1399 #009193ff
> color #4/1-3:2747-2799 lime
> color #4/1-3:2975-3055 #EF6B11
> color #4/1-3:2030-2190 #F4EB45
> color #4/1-3:3297-3329 #CE3674
> show nucleic
> hide protein|solvent|H
> surface hidePatches
> style (protein|nucleic|solvent) & @@draw_mode=0 stick
Changed 385230 atom styles
> cartoon
> cartoon style modeHelix default arrows true arrowsHelix false arrowScale 2
> width 2 thickness 0.4 sides 12 divisions 20
> cartoon style ~(nucleic|strand) xsection round
> cartoon style (nucleic|strand) xsection rectangle
> cartoon style protein modeHelix default arrows false xsection round width 2
> thickness 1
> cartoon style nucleic xsection round width 1.6 thickness 1.6
> nucleotides stubs radius 0.5
> size stickRadius 0.3
Changed 407138 bond radii
> hide #!4 models
> show #!4 models
> view name P5P1_front
> select #4/A:373,381,384
50 atoms, 47 bonds, 3 residues, 1 model selected
> select #B/A:373,381,384
Expected an objects specifier or a keyword
> select #4/B:373,381,384
45 atoms, 42 bonds, 3 residues, 1 model selected
> select add #4/A:55,19,21,332,333,350,349
155 atoms, 147 bonds, 10 residues, 1 model selected
> select add #4/1:499,432,381,542,379,413,2176,2112,2123,2103
349 atoms, 334 bonds, 20 residues, 1 model selected
> show sel
> hide H
> color sel byhetero
> select add #4
17636 atoms, 17798 bonds, 1 pseudobond, 1170 residues, 2 models selected
> select subtract #4
Nothing selected
> select add #4/1:499,432,381,542,379,413,2176,2112,2123,2103
194 atoms, 187 bonds, 10 residues, 1 model selected
> select #4/A:373,381,384
50 atoms, 47 bonds, 3 residues, 1 model selected
> select #4/B:373,381,384
45 atoms, 42 bonds, 3 residues, 1 model selected
> select add #4/A:55,19,21,332,333,350,349
155 atoms, 147 bonds, 10 residues, 1 model selected
> name sel residues frozen
"sel" is reserved and cannot be redefined
> name residues sel frozen
"sel frozen": contains extra trailing text
> name frozen residues sel
> select add #4
17636 atoms, 17798 bonds, 1 pseudobond, 1170 residues, 2 models selected
> select subtract #4
Nothing selected
> hide resides
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide residues
> select add #4/1:499,432,381,542,379,413,2176,2112,2123,2103
194 atoms, 187 bonds, 10 residues, 1 model selected
> select #4/A:373,381,384
50 atoms, 47 bonds, 3 residues, 1 model selected
> select #4/B:373,381,384
45 atoms, 42 bonds, 3 residues, 1 model selected
> select add #4/A:55,19,21,332,333,350,349
155 atoms, 147 bonds, 10 residues, 1 model selected
> select add #4/1:499,432,381,542,379,413,2176,2112,2123,2103
349 atoms, 334 bonds, 20 residues, 1 model selected
> select #4/A:373,381,384
50 atoms, 47 bonds, 3 residues, 1 model selected
> select #4/B:373,381,384
45 atoms, 42 bonds, 3 residues, 1 model selected
> select add #4/A:55,19,21,332,333,350,349
155 atoms, 147 bonds, 10 residues, 1 model selected
> select add #4/1:499,432,381,542,379,413,2176,2112,2123,2103
349 atoms, 334 bonds, 20 residues, 1 model selected
> name frozen residues sel
> hide residues
> select add #4
17636 atoms, 17798 bonds, 1 pseudobond, 1170 residues, 2 models selected
> select subtract #4
Nothing selected
> view list
Named views: P5P1_front, bottom_overview, diemr_1_close, dimer_1_close,
dimer_2_close, dimer_3_close, side_overview, side_overview_P5P1_dimer_2,
side_overview_P5P1_dimer_3
> view P5P1_front
> cd "/Users/lorenz.grundmann/VBC Dropbox/Group Folder
> Haselbach/Projects/HERC1/Lorenz/ChimeraX_session/PSCM5-PAAF1-Herc1"
Current working directory is: /Users/lorenz.grundmann/VBC Dropbox/Group Folder
Haselbach/Projects/HERC1/Lorenz/ChimeraX_session/PSCM5-PAAF1-Herc1
> spng overview.png
> save overview.png width 3000 height 3000 supersample 3 transparentBackground
> true
> show residuesz
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show residues
> hdie H
Unknown command: hdie H
> hide H
> select #4/A:373,381,384
50 atoms, 47 bonds, 3 residues, 1 model selected
> select #4/B:373,381,384
45 atoms, 42 bonds, 3 residues, 1 model selected
> select add #4/1:499,432
88 atoms, 84 bonds, 5 residues, 1 model selected
> name frozen RLD1-PSMC5 sel
> hide residues
> show RLD1-PSMC5
> hide H
> select add #4
17636 atoms, 17798 bonds, 1 pseudobond, 1170 residues, 2 models selected
> view list
Named views: P5P1_front, bottom_overview, diemr_1_close, dimer_1_close,
dimer_2_close, dimer_3_close, side_overview, side_overview_P5P1_dimer_2,
side_overview_P5P1_dimer_3
> view P5P1_front
> select subtract #4
Nothing selected
> ui tool show "Side View"
> view name RLD1-P5-interface
> select add #4/B:373@OE2
1 atom, 1 residue, 1 model selected
> select add #4
17636 atoms, 17798 bonds, 1 pseudobond, 1170 residues, 4 models selected
> select add #5
17636 atoms, 17798 bonds, 1 pseudobond, 1170 residues, 6 models selected
> select subtract #5
17636 atoms, 17798 bonds, 1 pseudobond, 1170 residues, 2 models selected
> select subtract #4
Nothing selected
> hide #!5 models
> select add #4/B:373@OE2
1 atom, 1 residue, 1 model selected
> select add #4/1:499@NZ
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.3 dashes 4
> hide #4.2 models
> close #4.2
> pbond sel color grey radius 0.2 dashes 4
> close #4.2
> pbond sel color grey radius 0.2 dashes 4 name RLD1-P5
> select subtract #4/1:499@NZ
1 atom, 1 residue, 1 model selected
> select subtract #4/B:373@OE2
Nothing selected
> select add #4/1:499@NZ
1 atom, 1 residue, 1 model selected
> select add #4/B:381@OE2
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 name RLD1-P5
> select add #4/B:384@OE1
3 atoms, 3 residues, 1 model selected
> select add #4
17636 atoms, 17798 bonds, 3 pseudobonds, 1170 residues, 3 models selected
> select subtract #4
Nothing selected
> select #4/B:384@OE1
1 atom, 1 residue, 1 model selected
> select add #4/1:432@OH
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 name RLD1-P5
> close #4.2
> pbond sel color grey radius 0.2 dashes 4 name RLD1-P5 showDist true
> hide #4.2.1 models
> show #4.2.1 models
> select #4/B:381@OE2
1 atom, 1 residue, 1 model selected
> select add #4/1:499@NZ
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 name RLD1-P5 showDist true
> select #4/B:373@OE2
1 atom, 1 residue, 1 model selected
> select add #4/1:499@NZ
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 name RLD1-P5 showDist true
> close #4.2
Cell requested for row 5 is out of bounds for table with 8 rows! Resizing
table model.
> pbond sel color grey radius 0.2 dashes 4 name RLD1-P5 showDist true reveal
> true
Cell requested for row 0 is out of bounds for table with 8 rows! Resizing
table model.
> pbond sel color grey radius 0.2 dashes 4 reveal true name RLD1-P5 showDist
> true
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> label sel
> close #4.3
> select #4/B:373@OE2
1 atom, 1 residue, 1 model selected
> select add #4/1:499@NZ
2 atoms, 2 residues, 1 model selected
> label sel
> select #4/1:499@NZ
1 atom, 1 residue, 1 model selected
> select add #4/B:381@OE2
2 atoms, 2 residues, 1 model selected
> label sel
> view list
Named views: P5P1_front, RLD1-P5-interface, bottom_overview, diemr_1_close,
dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view P5P1_front
> view RLD1-P5-interface
> select subtract #4/1:499@NZ
1 atom, 1 residue, 1 model selected
> select #4/1:499@NZ
1 atom, 1 residue, 1 model selected
> select add #4/B:381@OE2
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 reveal true name RLD1-P5 showDist
> true
> hide #!4.2 models
> hide #4.3 models
> show #4.3 models
> hide #4.3 models
> show #4.3 models
> hide #4.3 models
> close #4.3
> show #!4.2 models
> select #4/B:384@OE1
1 atom, 1 residue, 1 model selected
> select add #4/1:432@OH
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 reveal true name RLD1-P5 showDist
> true
> select #4/B:373@OE2
1 atom, 1 residue, 1 model selected
> select add #4/1:499@NZ
2 atoms, 2 residues, 1 model selected
> select add #4/B:381@OE2
3 atoms, 3 residues, 1 model selected
> select add #4/B:381@OE1
4 atoms, 3 residues, 1 model selected
> select #4/B:381@OE1
1 atom, 1 residue, 1 model selected
> select #4/B:373@OE2
1 atom, 1 residue, 1 model selected
> select add #4/B:381@OE2
2 atoms, 2 residues, 1 model selected
> select add #4/B:384@OE1
3 atoms, 3 residues, 1 model selected
> select add #4/1:432@OH
4 atoms, 4 residues, 1 model selected
> label sel name RLD1-P5
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> label sel
> show #!2 models
> hide #!2 models
> show #!5 models
> select add #4
17636 atoms, 17798 bonds, 5 pseudobonds, 1170 residues, 5 models selected
> select subtract #4
Nothing selected
> spng RLD1-P5_interaction.png
> save RLD1-P5_interaction.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #4.2.1 models
> hide #4.3 models
> spng RLD1-P5_interaction.png
> save RLD1-P5_interaction.png width 3000 height 3000 supersample 3
> transparentBackground true
> show #4.2.1 models
> show #4.3 models
> spng RLD1-P5_interaction_labelled.png
> save RLD1-P5_interaction_labelled.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #!4.2 models
> hide #4.2.1 models
> hide #4.3 models
> show residues
> hide H
> show #4
> color #4 byhetero
> hide H
> select #5
4 models selected
> select #4/1:674@OD2
1 atom, 1 residue, 1 model selected
> hide #!5 models
> select add #4/A:41@NE2
2 atoms, 2 residues, 1 model selected
> select up
29 atoms, 27 bonds, 2 residues, 1 model selected
> select up
175 atoms, 174 bonds, 13 residues, 1 model selected
> select down
29 atoms, 27 bonds, 2 residues, 1 model selected
> select down
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 reveal true name test
> pbond sel color grey radius 0.2 dashes 4 reveal true name test showDist true
> select #4/A:50@OE1
1 atom, 1 residue, 1 model selected
> select add #4/1:691@OD1
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 reveal true name test showDist true
> select add #4/A:39@CG2
3 atoms, 3 residues, 1 model selected
> select add #4/1:674@OD2
4 atoms, 4 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 reveal true name test showDist true
Must specify exactly 2 atoms to form pseudobond between; you specified 4
> select #4/A:19
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #4/A:39@CG2
1 atom, 1 residue, 1 model selected
> select add #4/1:674@OD2
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 reveal true name test showDist true
> close #4.4
> view list
Named views: P5P1_front, RLD1-P5-interface, bottom_overview, diemr_1_close,
dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view P5P1_front
> hide #4
> show residues
> hdie H
Unknown command: hdie H
> hide H
> view P5P1_front
> select add #4
17636 atoms, 17798 bonds, 5 pseudobonds, 1170 residues, 5 models selected
> select subtract #4
Nothing selected
> select #4/1:381@OG
1 atom, 1 residue, 1 model selected
> select add #4/1:379@OG
2 atoms, 2 residues, 1 model selected
> select add #4/A:19@OE1
3 atoms, 3 residues, 1 model selected
> select add #4/A:21@OE2
4 atoms, 4 residues, 1 model selected
> select add #4/1:413@OH
5 atoms, 5 residues, 1 model selected
> select add #4/A:55@OE1
6 atoms, 6 residues, 1 model selected
> select add #4/1:542@NH1
7 atoms, 7 residues, 1 model selected
> show #4.2.1 models
> hide #4.2.1 models
> show #4.3 models
> hide #4.3 models
> label sel
> show #4.3 models
> select add #4
17636 atoms, 17798 bonds, 5 pseudobonds, 1170 residues, 5 models selected
> select subtract #4
Nothing selected
> show #!5 models
> color zone #5 near #4 distance 6
> combine #4
> color #5/1 #BBBDBF
> hide #4.1 models
> show #4.1 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> color #6/1 #BBBDBF
> hide #!5 models
> hide #!4 models
> color #6/1-3:372-734 light sky blue
> color #6/1-3:3420-3820 #350CED
> color #6/1-3:3996-4366 #90CED6
> color #6/1-3:4447-4840 #d31340ff
> color #6/1-3:2315-2379 palegreen
> color #6/1-3:1384-1399 #009193ff
> color #6/1-3:2747-2799 lime
> color #6/1-3:2975-3055 #EF6B11
> color #6/1-3:2030-2190 #F4EB45
> color #6/1-3:3297-3329 #CE3674
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> color #6 bychain
> color #6/1 #BBBDBF
> color #6/1-3:372-734 light sky blue
> color #6/1-3:3420-3820 #350CED
> color #6/1-3:3996-4366 #90CED6
> color #6/1-3:4447-4840 #d31340ff
> color #6/1-3:2315-2379 palegreen
> color #6/1-3:1384-1399 #009193ff
> color #6/1-3:2747-2799 lime
> color #6/1-3:2975-3055 #EF6B11
> color #6/1-3:2030-2190 #F4EB45
> color #6/1-3:3297-3329 #CE3674
> hide #6
> show nucleic
> hide protein|solvent|H
> surface hidePatches
> style (protein|nucleic|solvent) & @@draw_mode=0 stick
Changed 0 atom styles
> cartoon
> cartoon style modeHelix default arrows true arrowsHelix false arrowScale 2
> width 2 thickness 0.4 sides 12 divisions 20
> cartoon style ~(nucleic|strand) xsection round
> cartoon style (nucleic|strand) xsection rectangle
> cartoon style protein modeHelix default arrows false xsection round width 2
> thickness 1
> cartoon style nucleic xsection round width 1.6 thickness 1.6
> nucleotides stubs radius 0.5
> size stickRadius 0.3
Changed 424936 bond radii
> color #6 #7b68ee7e
> undo
> transparency #6 50
> transparency #6 50color #6 tr 50
Missing or invalid "percent" argument: Expected a number
> color #6 transparency 50
> show #!5 models
> show #!4 models
> color zone #5 near #6 distance 6
> transparency #5 50
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> shpw residues
Unknown command: shpw residues
> show residues
> hide H
> select add #4/1:381@OG
1 atom, 1 residue, 1 model selected
> select add #4/1:379@OG
2 atoms, 2 residues, 1 model selected
> select add #4/1:413@OH
3 atoms, 3 residues, 1 model selected
> select add #4/A:19@OE1
4 atoms, 4 residues, 1 model selected
> select add #4/A:21@OE1
5 atoms, 5 residues, 1 model selected
> select add #4/A:55@OE2
6 atoms, 6 residues, 1 model selected
> select add #4/1:542@NH1
7 atoms, 7 residues, 1 model selected
> select #4/1:542@NH1
1 atom, 1 residue, 1 model selected
> select add #4/A:55@OE2
2 atoms, 2 residues, 1 model selected
> select add #4/A:21@OE1
3 atoms, 3 residues, 1 model selected
> select add #4/A:19@OE1
4 atoms, 4 residues, 1 model selected
> select add #4/1:381@OG
5 atoms, 5 residues, 1 model selected
> select add #4/1:379@OG
6 atoms, 6 residues, 1 model selected
> select add #4/1:413@OH
7 atoms, 7 residues, 1 model selected
> select up
112 atoms, 106 bonds, 7 residues, 1 model selected
> name frozen sel RLD1-P1
Missing or invalid "objects" argument: invalid objects specifier
> name frozen RLD1-P1 sel
> select add #4
17636 atoms, 17798 bonds, 5 pseudobonds, 1170 residues, 5 models selected
> select subtract #4
Nothing selected
> show #!5 models
> color zone #5 near #6 distance 6
> transparency #5 50
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> color #6/B #ABAA00
> color zone #5 near #6 distance 6
> transparency #5 50
> show #!5 models
> color zone #5 near #6 distance 6
> transparency #5 50
> volume #5 level 0.1811
> transparency #5 50
> color zone #5 near #6 distance 6
> transparency #5 50
> hide #!5 models
> select clear
> select #4/1:381@OG
1 atom, 1 residue, 1 model selected
> select add #4/A:19@OE1
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 reveal true name RLD1-P1 showDist
> true
> select #4/1:379@OG
1 atom, 1 residue, 1 model selected
> select add #4/A:19@OE2
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 reveal true name RLD1-P1 showDist
> true
> select #4/1:413@OH
1 atom, 1 residue, 1 model selected
> select add #4/A:21@OE2
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 reveal true name RLD1-P1 showDist
> true
> select #4/A:55@OE2
1 atom, 1 residue, 1 model selected
> select add #4/1:542@NH1
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 reveal true name RLD1-P1 showDist
> true
> show #!5 models
> transparency #5 50
> color zone #5 near #6 distance 6
> transparency #5 50
> volume #5 level 0.2294
> color zone #5 near #6 distance 6
> transparency #5 50
> select add #4
17636 atoms, 17798 bonds, 9 pseudobonds, 1170 residues, 7 models selected
> select subtract #4
Nothing selected
> color zone #5 near #6 distance 6
> transparency #5 50
> spng RLD1-P1_interaction_labelled.png
> save RLD1-P1_interaction_labelled.png width 3000 height 3000 supersample 3
> transparentBackground true
> graphics silhouettes true width 4
> graphics silhouettes true width 8
> spng RLD1-P1_interaction_labelled.png
> save RLD1-P1_interaction_labelled.png width 3000 height 3000 supersample 3
> transparentBackground true
> graphics silhouettes true width 4
> graphics silhouettes true width 6
> view list
Named views: P5P1_front, RLD1-P5-interface, bottom_overview, diemr_1_close,
dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view P5P1_front
> spng RLD1-P1_interaction-1_labelled.png
> save RLD1-P1_interaction-1_labelled.png width 3000 height 3000 supersample 3
> transparentBackground true
> color zone #5 near #6 distance 6
> transparency #5 50
> select #4/1:728
11 atoms, 10 bonds, 1 residue, 1 model selected
> select resideus
Expected an objects specifier or a keyword
> select residues
Missing "residues" keyword's argument
> name list
RLD1-P1 [112 atoms, 212 bonds]
RLD1-PSMC5 [88 atoms, 168 bonds]
residues [349 atoms, 668 bonds]
> select residues
Missing "residues" keyword's argument
> show residues
> hide residues
> name
Missing or invalid "name" argument: Expected a text string
> select #4/A:373,381,384
50 atoms, 47 bonds, 3 residues, 1 model selected
> select #4/B:373,381,384
45 atoms, 42 bonds, 3 residues, 1 model selected
> select add #4/A:55,19,21,332,333,350,349
155 atoms, 147 bonds, 10 residues, 1 model selected
> select add #4/1:499,432,381,542,379,413,2176,2112,2123,2103
349 atoms, 334 bonds, 20 residues, 1 model selected
> select add #4/1:728
360 atoms, 344 bonds, 21 residues, 1 model selected
> show sel
> view name RLD1-P1_interaction-1
> select #4/A:19@OE2
1 atom, 1 residue, 1 model selected
> select add #4/1:728@HG
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 reveal true name RLD1-P1 showDist
> true
> view list
Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P5-interface,
bottom_overview, diemr_1_close, dimer_1_close, dimer_2_close, dimer_3_close,
side_overview, side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view P5P1_front
> show
> hide
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!4 models
> hide #!5 models
> color #6/B #ABAA00
> color #6/A #363600
> hide #!6 models
> select add #4/1:728
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #4/A:373,381,384
50 atoms, 47 bonds, 3 residues, 1 model selected
> select #4/B:373,381,384
45 atoms, 42 bonds, 3 residues, 1 model selected
> select add #4/A:55,19,21,332,333,350,349
155 atoms, 147 bonds, 10 residues, 1 model selected
> select add #4/1:499,432,381,542,379,413,2176,2112,2123,2103
349 atoms, 334 bonds, 20 residues, 1 model selected
> show #!6 models
> hide #!6 models
> show #!4 models
> name frozen residues sel
> view list
Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P5-interface,
bottom_overview, diemr_1_close, dimer_1_close, dimer_2_close, dimer_3_close,
side_overview, side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view RLD1-P1_interaction-1
> show residues
> hide H
> select add #4
17636 atoms, 17798 bonds, 10 pseudobonds, 1170 residues, 7 models selected
> select subtract #4
Nothing selected
> show #!5 models
> select add #4/1:499,432,381,542,379,413,2176,2112,2123,2103
194 atoms, 187 bonds, 10 residues, 1 model selected
> select #4/A:373,381,384
50 atoms, 47 bonds, 3 residues, 1 model selected
> select #4/B:373,381,384
45 atoms, 42 bonds, 3 residues, 1 model selected
> select add #4/A:55,19,21,332,333,350,349
155 atoms, 147 bonds, 10 residues, 1 model selected
> select add #4/1:728
166 atoms, 157 bonds, 11 residues, 1 model selected
> name frozen residues sel
> show residues
> hide H
> select #4/A:19@OE2
1 atom, 1 residue, 1 model selected
> select add #4/1:728@OG
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 reveal true name RLD1-P1 showDist
> true
> view list
Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P5-interface,
bottom_overview, diemr_1_close, dimer_1_close, dimer_2_close, dimer_3_close,
side_overview, side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view RLD1-P1_interaction-1
> color zone #5 near #6 distance 6
> transparency #5 50
> select add #4
17636 atoms, 17798 bonds, 11 pseudobonds, 1170 residues, 7 models selected
> select subtract #4
Nothing selected
> spng RLD1-P1_interaction-1_labelled.png
> save RLD1-P1_interaction-1_labelled.png width 3000 height 3000 supersample 3
> transparentBackground true
> view RLD1-P1_interaction-1
[Repeated 1 time(s)]
> color zone #5 near #6 distance 6
> transparency #5 50
> spng RLD1-P1_interaction-2_labelled.png
> save RLD1-P1_interaction-2_labelled.png width 3000 height 3000 supersample 3
> transparentBackground true
> transparency #5 50
> color zone #5 near #6 distance 6
> transparency #5 50
> color zone #5 near #6 distance 6
> transparency #5 50
> spng RLD1-P1_interaction-2_labelled.png
> save RLD1-P1_interaction-2_labelled.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #4.3 models
> hide #4.4.1 models
> color zone #5 near #6 distance 6
> transparency #5 50
> spng RLD1-P1_interaction-2.png
> save RLD1-P1_interaction-2.png width 3000 height 3000 supersample 3
> transparentBackground true
> view list
Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P5-interface,
bottom_overview, diemr_1_close, dimer_1_close, dimer_2_close, dimer_3_close,
side_overview, side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view name RLD1-P1_interaction-2
> view RLD1-P1_interaction-1
> transparency #5 50
> color zone #5 near #6 distance 6
> transparency #5 50
> spng RLD1-P1_interaction-1.png
> save RLD1-P1_interaction-1.png width 3000 height 3000 supersample 3
> transparentBackground true
> view list
Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
RLD1-P5-interface, bottom_overview, diemr_1_close, dimer_1_close,
dimer_2_close, dimer_3_close, side_overview, side_overview_P5P1_dimer_2,
side_overview_P5P1_dimer_3
> view RLD1-P1_interaction-2
> view name RLD1-P1_interaction-1
> color zone #5 near #6 distance 6
> transparency #5 50
> spng RLD1-P1_interaction-2.png
> save RLD1-P1_interaction-2.png width 3000 height 3000 supersample 3
> transparentBackground true
> show #4.4.1 models
> show #4.3 models
> spng RLD1-P1_interaction-2_labelled.png
> save RLD1-P1_interaction-2_labelled.png width 3000 height 3000 supersample 3
> transparentBackground true
> color zone #5 near #6 distance 6
> transparency #5 50
> spng RLD1-P1_interaction-2_labelled.png
> save RLD1-P1_interaction-2_labelled.png width 3000 height 3000 supersample 3
> transparentBackground true
> view list
Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
RLD1-P5-interface, bottom_overview, diemr_1_close, dimer_1_close,
dimer_2_close, dimer_3_close, side_overview, side_overview_P5P1_dimer_2,
side_overview_P5P1_dimer_3
> view P5P1_front
> volume #5 level 0.1714
> hide #!5 models
> show #!5 models
> volume #5 level 0.2488
> volume #5 level 0.2004
> select #5
4 models selected
> hide #!5 models
> select #4/A:349@NE2
1 atom, 1 residue, 1 model selected
> select add #4/1:2176@OH
2 atoms, 2 residues, 1 model selected
> select up
38 atoms, 37 bonds, 2 residues, 1 model selected
> name frozen SPRY-P1_1
Missing or invalid "objects" argument: empty atom specifier
> name frozen SPRY-P1_1 sel
> hide residues
> show SPRY-P1_1
> hide H
> hide residues
> name list
RLD1-P1 [112 atoms, 212 bonds]
RLD1-PSMC5 [88 atoms, 168 bonds]
SPRY-P1_1 [38 atoms, 74 bonds]
residues [166 atoms, 314 bonds]
> hide al
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide al
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide all
> show residues
> hide residues
> select #4/B:373,381,384
45 atoms, 42 bonds, 3 residues, 1 model selected
> select add #4/A:55,19,21,332,333,350,349
155 atoms, 147 bonds, 10 residues, 1 model selected
> select add #4/1:728
166 atoms, 157 bonds, 11 residues, 1 model selected
> select add #4/1:499,432,381,542,379,413,2176,2112,2123,2103
360 atoms, 344 bonds, 21 residues, 1 model selected
> name frozen residues sel
> show residues
> hide residues
> show SPRY-P1_1
> hide H
> show #!5 models
> select add #4
17636 atoms, 17798 bonds, 11 pseudobonds, 1170 residues, 7 models selected
> select subtract #4
Nothing selected
> hide #!5 models
> select #4/A:349@NE2
1 atom, 1 residue, 1 model selected
> select add #4/1:2176@OH
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 reveal true name SPRY-P1-1 showDist
> true
> label sel
> show #!5 models
> color zone #5 near #6 distance 6
> transparency #5 50
> spng SPRY-P1_1_labelled.png
> save SPRY-P1_1_labelled.png width 3000 height 3000 supersample 3
> transparentBackground true
> select add #4
17636 atoms, 17798 bonds, 12 pseudobonds, 1170 residues, 9 models selected
> select subtract #4
Nothing selected
> color zone #5 near #6 distance 6
> transparency #5 50
> spng SPRY-P1_1_labelled.png
> save SPRY-P1_1_labelled.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #4.4.1 models
> hide #4.3 models
> spng SPRY-P1_1.png
> save SPRY-P1_1.png width 3000 height 3000 supersample 3
> transparentBackground true
> color zone #5 near #6 distance 6
> transparency #5 50
> color zone #5 near #6 distance 6
> transparency #5 50
> spng SPRY-P1_1.png
> save SPRY-P1_1.png width 3000 height 3000 supersample 3
> transparentBackground true
> show #4.4.1 models
> hide #4.4.1 models
> show #4.3 models
> color zone #5 near #6 distance 6
> transparency #5 50
> spng SPRY-P1_1_labelled.png
> save SPRY-P1_1_labelled.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #4.3 models
> hide #4.5.1 models
> spng SPRY-P1_1.png
> save SPRY-P1_1.png width 3000 height 3000 supersample 3
> transparentBackground true
> view name SPRY-P1_1
> show residues
> hide H
> name list
RLD1-P1 [112 atoms, 212 bonds]
RLD1-PSMC5 [88 atoms, 168 bonds]
SPRY-P1_1 [38 atoms, 74 bonds]
residues [360 atoms, 688 bonds]
> hide SPRY-P1_1
> volume #5 level 0.1811
> color zone #5 near #6 distance 6
> transparency #5 50
> hide #!5 models
> hide SPRY-P1_2
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> view name SPRY-P1_2
> show #!5 models
> select #4/A:332@NH1
1 atom, 1 residue, 1 model selected
> select add #4/1:2123@OE1
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 reveal true name SPRY-P1-2 showDist
> true
> select #4/1:2123@OE2
1 atom, 1 residue, 1 model selected
> select add #4/A:333@OD1
2 atoms, 2 residues, 1 model selected
> select #4/1:2103@NH2
1 atom, 1 residue, 1 model selected
> select add #4/A:333@OD2
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 reveal true name SPRY-P1-2 showDist
> true
> select #4/1:2112@NH1
1 atom, 1 residue, 1 model selected
> select add #4/A:350@OD1
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 reveal true name SPRY-P1-2 showDist
> true
> select #4/1:2103@NH1
1 atom, 1 residue, 1 model selected
> select add #4/A:350@OD1
2 atoms, 2 residues, 1 model selected
> pbond sel color grey radius 0.2 dashes 4 reveal true name SPRY-P1-2 showDist
> true
> hide #!5 models
> select add #4/1:2112@NH1
3 atoms, 3 residues, 1 model selected
> select add #4/A:333@OD2
4 atoms, 4 residues, 1 model selected
> select add #4/1:2123@OE2
5 atoms, 5 residues, 1 model selected
> select add #4/A:332@NH1
6 atoms, 6 residues, 1 model selected
> select up
111 atoms, 106 bonds, 6 residues, 1 model selected
> name frozen SPRY-P1_12 sel
> name frozen SPRY-P1_2 sel
> name remove SPRY-P1_2
> name remove SPRY-P1_12
> name frozen SPRY-P1_2 sel
> show #!5 models
> volume #5 level 0.1908
> color zone #5 near #6 distance 6
> transparency #5 50
> select add #4
17636 atoms, 17798 bonds, 16 pseudobonds, 1170 residues, 11 models selected
> select subtract #4
Nothing selected
> spng SPRY-P1_2_labelled.png
> save SPRY-P1_2_labelled.png width 3000 height 3000 supersample 3
> transparentBackground true
> select #4/1:2103@NH2
1 atom, 1 residue, 1 model selected
> select #4/A:350@OD1
1 atom, 1 residue, 1 model selected
> select add #4/1:2103@NH2
2 atoms, 2 residues, 1 model selected
> select add #5
2 atoms, 2 residues, 5 models selected
> select subtract #5
2 atoms, 2 residues, 1 model selected
> hide #!5 models
> select add #4/1:2112@NH1
3 atoms, 3 residues, 1 model selected
> select add #4/1:2112@NH2
4 atoms, 3 residues, 1 model selected
> select add #4/A:333@OD2
5 atoms, 4 residues, 1 model selected
> select add #4/1:2123@OE1
6 atoms, 5 residues, 1 model selected
> select add #4/A:332@NH1
7 atoms, 6 residues, 1 model selected
> label sel
> show #4.3 models
> hide #4.3 models
> show #4.3 models
> hide #!4.6 models
> show #!4.6 models
> hide #4.3 models
> show #4.3 models
> hide #4.3 models
> show #4.3 models
> hide #!4.6 models
> show #!4.6 models
> show #!5 models
> color zone #5 near #6 distance 6
> transparency #5 50
> spng SPRY-P1_2_labelled.png
> save SPRY-P1_2_labelled.png width 3000 height 3000 supersample 3
> transparentBackground true
> select add #4
17636 atoms, 17798 bonds, 16 pseudobonds, 1170 residues, 11 models selected
> select subtract #4
Nothing selected
> spng SPRY-P1_2_labelled.png
> save SPRY-P1_2_labelled.png width 3000 height 3000 supersample 3
> transparentBackground true
> hide #!4.6 models
> show #!4.6 models
> hide #4.6.1 models
> hide #4.3 models
> spng SPRY-P1_2.png
> save SPRY-P1_2.png width 3000 height 3000 supersample 3
> transparentBackground true
> save 20260203_interactions.cxs
> view list
Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
RLD1-P5-interface, SPRY-P1_1, SPRY-P1_2, bottom_overview, diemr_1_close,
dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view P5P1_front
> volume #5 level 0.2294
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!5 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!2 models
> show #!3 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> show #!1 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> show #!3 models
> hide #!1 models
> show #!2 models
> view list
Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
RLD1-P5-interface, SPRY-P1_1, SPRY-P1_2, bottom_overview, diemr_1_close,
dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view P5P1_front
> vop copy #2
Opened 20260203_frankemnmap.mrc copy as #7, grid size 360,360,360, pixel 1.27,
shown at step 1, values float32
> hide #!3 models
> show #!3 models
> color zone #7 near #3 distance 6
> hide #!7 models
> show #!7 models
> hide #!4.6 models
> hide #!7 models
> show #!7 models
> hide #4.1 models
> hide #!3 models
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/lorenz.grundmann/Desktop/movie1.mp4
Movie saved to /Users/lorenz.grundmann/Desktop/movie1.mp4
> view #7 clip false
> save /Users/lorenz.grundmann/Desktop/image1.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/lorenz.grundmann/Desktop/movie2.mp4
Movie saved to /Users/lorenz.grundmann/Desktop/movie2.mp4
> view list
Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
RLD1-P5-interface, SPRY-P1_1, SPRY-P1_2, bottom_overview, diemr_1_close,
dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view bottom_overview
> spng bottom.png
> save bottom.png width 3000 height 3000 supersample 3 transparentBackground
> true
> view side_overview_P5P1_dimer_2
> view side_overview_P5P1_dimer_3
> view side_overview
> spng side.png
> save side.png width 3000 height 3000 supersample 3 transparentBackground
> true
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/lorenz.grundmann/Desktop/movie3.mp4
Movie saved to /Users/lorenz.grundmann/Desktop/movie3.mp4
> hide #!7 models
> show #!3 models
> graphics silhouettes true width 4
> view list
Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
RLD1-P5-interface, SPRY-P1_1, SPRY-P1_2, bottom_overview, diemr_1_close,
dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view P5P1_front
> hide #!4.2 models
> show #!4.2 models
> hide #!4.2 models
> show #!4.2 models
> show #4.1 models
> hide #!4 models
> mathc #3 to #4
Unknown command: mathc #3 to #4
> matchmaker #3 to #4
Computing secondary structure
[Repeated 1 time(s)] 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 20260114_P5P1_new-fit.cif, chain A (#4) with copy of
20260203_frankemnmodel.pdb, chain A (#3), sequence alignment score = 2024.9
RMSD between 392 pruned atom pairs is 0.320 angstroms; (across all 392 pairs:
0.320)
> hide #4.1 models
> show #4.1 models
> hide #!3 models
> show #!3 models
> hide #4.1 models
> show #4.1 models
> hide #!4 models
> view list
Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
RLD1-P5-interface, SPRY-P1_1, SPRY-P1_2, bottom_overview, diemr_1_close,
dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view side_overview
> hide #3/2 cartoons
> hide #3/C-f
> hide #3/C-F
> hide #3/C-F cartoons
> hide #3/3:370-738
> hide #3/3:370-738 cartoons
> color #3/1-3:3996-4366 #0437FF
> undo
> color #3/1-3:3420-3820 #0437FF
[Repeated 1 time(s)]
> show #!2 models
> hide #!2 models
> show #!7 models
> hide #!3 models
> show #!3 models
> hide #!7 models
> show #!7 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!3 models
> color zone #7 near #3 distance 6
> hide #!7 models
> show #!2 models
> hide #!3 models
> view list
Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
RLD1-P5-interface, SPRY-P1_1, SPRY-P1_2, bottom_overview, diemr_1_close,
dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view side_overview
> side.png
Unknown command: side.png
> spng side.png
> save side.png width 3000 height 3000 supersample 3 transparentBackground
> true
> view bottom_overview
> spng bottom.png
> save bottom.png width 3000 height 3000 supersample 3 transparentBackground
> true
> hide #!2 models
> color #1/A #363600
> color #1/B #ABAA00
> color #1/E #005A4A
> color #1/F #2CC9A6
> color #1/C #1F2A44
> color #1/D #5B7DBB
> show #!1 models
> color #3/A #363600
> color #3/B #ABAA00
> color #3/E #005A4A
> color #3/F #2CC9A6
> color #3/C #3F2A44
> color #3/D #5B7DBB
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!1 models
> color zone #2 near #1 distance 6
> view list
Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
RLD1-P5-interface, SPRY-P1_1, SPRY-P1_2, bottom_overview, diemr_1_close,
dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view bottom_overview
> spng bottom.png
> save bottom.png width 3000 height 3000 supersample 3 transparentBackground
> true
Cell requested for row 0 is out of bounds for table with 17 rows! Resizing
table model.
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> view side_overview
> spng side.png
> save side.png width 3000 height 3000 supersample 3 transparentBackground
> true
> hide #!2 models
> show #!1 models
> show #!7 models
> hide #!7 models
> hide #!1 models
> show #!1 models
> show #!3 models
> hide #!1 models
> view list
Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
RLD1-P5-interface, SPRY-P1_1, SPRY-P1_2, bottom_overview, diemr_1_close,
dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view side_overview
> view list
Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
RLD1-P5-interface, SPRY-P1_1, SPRY-P1_2, bottom_overview, diemr_1_close,
dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view side_overview
> hide #2 cartoons
> hide #3/2 cartoons
> hide #3/3 cartoons
> view list
Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
RLD1-P5-interface, SPRY-P1_1, SPRY-P1_2, bottom_overview, diemr_1_close,
dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view side_overview
[Repeated 1 time(s)]
> spng protomer_P5P1.png
> save protomer_P5P1.png width 3000 height 3000 supersample 3
> transparentBackground true
> turn z 180
[Repeated 3 time(s)]
> turn y 180
> spng protomer_P5P1_180.png
> save protomer_P5P1_180.png width 3000 height 3000 supersample 3
> transparentBackground true
> view list
Named views: P5P1_front, RLD1-P1_interaction-1, RLD1-P1_interaction-2,
RLD1-P5-interface, SPRY-P1_1, SPRY-P1_2, bottom_overview, diemr_1_close,
dimer_1_close, dimer_2_close, dimer_3_close, side_overview,
side_overview_P5P1_dimer_2, side_overview_P5P1_dimer_3
> view side_overview
> view side_overview_P5P1_dimer_3
> view side_overview
> shpw #3/3 cartoon
Unknown command: shpw #3/3 cartoon
> show #3/3 cartoons
> spng protomer_2_P5P1_180.png
> save protomer_2_P5P1_180.png width 3000 height 3000 supersample 3
> transparentBackground true
> save 20260203_interactions.cxs includeMaps true
——— End of log from Tue Feb 3 16:26:41 2026 ———
> view name session-start
opened ChimeraX session
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M3 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,9
Model Number: MUW63D/A
Chip: Apple M3 Max
Total Number of Cores: 16 (12 performance and 4 efficiency)
Memory: 48 GB
System Firmware Version: 13822.41.1
OS Loader Version: 13822.41.1
Software:
System Software Overview:
System Version: macOS 26.1 (25B78)
Kernel Version: Darwin 25.1.0
Time since boot: 1 day, 10 hours, 17 minutes
Graphics/Displays:
Apple M3 Max:
Chipset Model: Apple M3 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 40
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
DELL S2722QC:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.6.1
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.19
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-Clipper: 0.25.2
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ISOLDE: 1.10.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
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-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
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: 1.1.3
ChimeraX-ProfileGrids: 1.1.3
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-rRNA-Inspector: 0.93
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.10.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.15
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.3.2
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.1
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
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