![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 weeks ago
Last modified 4 weeks ago
#19284 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.7.6-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00007ff852865a00 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.compiled, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, 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, PIL._imagingmath (total: 61)
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{
"uptime" : 170000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"coalitionID" : 6843,
"osVersion" : {
"train" : "macOS 13.7.6",
"build" : "22H625",
"releaseType" : "User"
},
"captureTime" : "2025-11-03 21:36:52.5951 -0500",
"incident" : "B6771A0F-FC2C-4C36-AF8A-02E4481F3410",
"pid" : 5503,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-11-03 16:24:56.9945 -0500",
"procStartAbsTime" : 160790330429963,
"procExitAbsTime" : 173835879582543,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"ED384F36-3934-52A1-9ECF-177702680592","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "78B83D24-5FA1-CEDC-7626-A65A78D8D801",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 51,
"bridgeVersion" : {"build":"22P5072","train":"9.5"},
"sleepWakeUUID" : "511D2CB0-6A89-491F-8038-09A3BB7C0049",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4548145152\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10f173000-10f177000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":5503},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4548145152\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10f173000-10f177000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/comparison_processing_2024_2025_withdocking_residues.cxs
Opened denmod_map_sharpened.ccp4 as #4, grid size 97,111,122, pixel 1.24,
shown at level 1.37, step 1, values float32
Opened cryosparc_P24_J221_volume_map_consensus.mrc as #5, grid size
144,144,144, pixel 2.86, shown at level 0.696, step 1, values float32
Opened cryosparc_P27_J86_004_volume_map.mrc as #3, grid size 256,256,256,
pixel 1.33, shown at level 0.12, step 1, values float32
Opened cryosparc_P27_J169_006_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 1.33, shown at level 0.624, step 1, values float32
Opened denmod_map_sharpened.ccp4 as #8, grid size 256,256,256, pixel 1.33,
shown at level 0.115, step 1, values float32
Opened cryosparc_P27_J141_flex_map.mrc as #10, grid size 256,256,256, pixel
1.33, shown at level 0.00547, step 1, values float32
Opened cryosparc_P24_J249_010_volume_map_sharp_resampled.mrc as #13, grid size
97,111,122, pixel 1.24,1.24,1.24, shown at level 0.879, step 1, values float32
Log from Mon Nov 3 13:41:56 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/comparison_processing_2024_2025.cxs
Opened denmod_map_sharpened.ccp4 as #4, grid size 97,111,122, pixel 1.24,
shown at level 1.37, step 1, values float32
Opened cryosparc_P24_J221_volume_map_consensus.mrc as #5, grid size
144,144,144, pixel 2.86, shown at level 0.696, step 1, values float32
Opened cryosparc_P27_J86_004_volume_map.mrc as #3, grid size 256,256,256,
pixel 1.33, shown at level 0.102, step 1, values float32
Opened cryosparc_P27_J169_006_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 1.33, shown at level 0.624, step 1, values float32
Opened denmod_map_sharpened.ccp4 as #8, grid size 256,256,256, pixel 1.33,
shown at level 0.115, step 1, values float32
Opened cryosparc_P27_J141_flex_map.mrc as #10, grid size 256,256,256, pixel
1.33, shown at level 0.00547, step 1, values float32
Log from Mon Nov 3 11:59:03 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/comparison_processing_2024_2025.cxs
Opened denmod_map_sharpened.ccp4 as #4, grid size 97,111,122, pixel 1.24,
shown at level 1.37, step 1, values float32
Opened cryosparc_P24_J221_volume_map_consensus.mrc as #5, grid size
144,144,144, pixel 2.86, shown at level 0.696, step 1, values float32
Opened cryosparc_P27_J86_004_volume_map.mrc as #3, grid size 256,256,256,
pixel 1.33, shown at level 0.102, step 1, values float32
Opened cryosparc_P27_J169_006_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 1.33, shown at level 0.624, step 1, values float32
Opened denmod_map_sharpened.ccp4 as #8, grid size 256,256,256, pixel 1.33,
shown at level 0.115, step 1, values float32
Opened cryosparc_P27_J141_flex_map.mrc as #10, grid size 256,256,256, pixel
1.33, shown at level 0.00547, step 1, values float32
Opened cryosparc_P24_J249_010_volume_map_sharp_resampled.mrc as #13.1.1.1,
grid size 97,111,122, pixel 1.24,1.24,1.24, shown at level 2.07, step 1,
values float32
Log from Mon Nov 3 11:46:56 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/comparison_processing_2024_2025.cxs
Opened cryosparc_P24_J249_010_volume_map_sharp_resampled.mrc as #2, grid size
97,111,122, pixel 1.24,1.24,1.24, shown at level 1.82, step 1, values float32
Opened denmod_map_sharpened.ccp4 as #4, grid size 97,111,122, pixel 1.24,
shown at level 1.37, step 1, values float32
Opened cryosparc_P24_J221_volume_map_consensus.mrc as #5, grid size
144,144,144, pixel 2.86, shown at level 0.845, step 1, values float32
Opened cryosparc_P27_J86_004_volume_map.mrc as #3, grid size 256,256,256,
pixel 1.33, shown at level 0.11, step 1, values float32
Opened cryosparc_P27_J169_006_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 1.33, shown at level 0.516, step 1, values float32
Opened denmod_map_sharpened.ccp4 as #8, grid size 256,256,256, pixel 1.33,
shown at level 0.115, step 1, values float32
Opened cryosparc_P27_J141_flex_map.mrc as #10, grid size 256,256,256, pixel
1.33, shown at level 0.00547, step 1, values float32
Log from Thu Sep 18 21:45:21 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/comparison_processing_2024_2025.cxs
Opened cryosparc_P24_J249_010_volume_map_sharp_resampled.mrc as #2, grid size
97,111,122, pixel 1.24,1.24,1.24, shown at level 0.733, step 1, values float32
Opened denmod_map_sharpened.ccp4 as #4, grid size 97,111,122, pixel 1.24,
shown at level 0.373, step 1, values float32
Opened cryosparc_P24_J221_volume_map_consensus.mrc as #5, grid size
144,144,144, pixel 2.86, shown at level 0.758, step 1, values float32
Opened cryosparc_P27_J86_004_volume_map.mrc as #3, grid size 256,256,256,
pixel 1.33, shown at level 0.11, step 1, values float32
Opened cryosparc_P27_J169_006_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 1.33, shown at level 0.287, step 1, values float32
Opened denmod_map_sharpened.ccp4 as #8, grid size 256,256,256, pixel 1.33,
shown at level 0.062, step 1, values float32
Opened cryosparc_P27_J141_flex_map.mrc as #10, grid size 256,256,256, pixel
1.33, shown at level 0.00547, step 1, values float32
Log from Mon Aug 18 17:27:18 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/Serinc5Ap2Nef_project_maps_withdocking_04172025.cxs
Opened cryosparc_P24_J249_010_volume_map_sharp_resampled.mrc as #2, grid size
97,111,122, pixel 1.24,1.24,1.24, shown at level 1.31, step 1, values float32
Opened denmod_map_sharpened.ccp4 as #4, grid size 97,111,122, pixel 1.24,
shown at level 1.74, step 1, values float32
Opened cryosparc_P24_J249_010_volume_map_resampled.mrc as #3, grid size
97,111,122, pixel 1.24,1.24,1.24, shown at level 0.762, step 1, values float32
Opened cryosparc_P24_J221_volume_map_consensus.mrc as #5, grid size
144,144,144, pixel 2.86, shown at level 0.758, step 1, values float32
Log from Thu Apr 17 14:19:45 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/Serinc5Ap2Nef_project_maps_models_03032025.cxs
Opened cryosparc_P24_J249_010_volume_map_sharp_resampled.mrc as #2, grid size
97,111,122, pixel 1.24,1.24,1.24, shown at level 1.23, step 1, values float32
Opened denmod_map_sharpened.ccp4 as #4, grid size 97,111,122, pixel 1.24,
shown at level 0.644, step 1, values float32
Opened cryosparc_P24_J249_010_volume_map_resampled.mrc as #3, grid size
97,111,122, pixel 1.24,1.24,1.24, shown at level 0.916, step 1, values float32
Opened cryosparc_P24_J221_volume_map_consensus.mrc as #5, grid size
144,144,144, pixel 2.86, shown at level 1.73, step 1, values float32
Log from Sun Mar 2 22:52:36 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/Serinc5Ap2Nef_project_maps_models_02252025.cxs
Opened cryosparc_P24_J249_010_volume_map_sharp_resampled.mrc as #2, grid size
97,111,122, pixel 1.24,1.24,1.24, shown at level 1.23, step 1, values float32
Opened denmod_map_sharpened.ccp4 as #4, grid size 97,111,122, pixel 1.24,
shown at level 0.644, step 1, values float32
Opened cryosparc_P24_J249_010_volume_map_resampled.mrc as #3, grid size
97,111,122, pixel 1.24,1.24,1.24, shown at level 0.916, step 1, values float32
Opened cryosparc_P24_J221_volume_map_consensus.mrc as #5, grid size
144,144,144, pixel 2.86, shown at level 1.73, step 1, values float32
Log from Tue Feb 25 18:08:00 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/Serinc5Ap2Nef_project_02112025.cxs
Opened cryosparc_P24_J249_010_volume_map_sharp_resampled.mrc as #2, grid size
97,111,122, pixel 1.24,1.24,1.24, shown at level 1.23, step 1, values float32
Opened denmod_map_sharpened.ccp4 as #4, grid size 97,111,122, pixel 1.24,
shown at level 1.29, step 1, values float32
Opened cryosparc_P24_J249_010_volume_map_resampled.mrc as #3, grid size
97,111,122, pixel 1.24,1.24,1.24, shown at level 0.587, step 1, values float32
Log from Tue Feb 11 16:42:50 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/bestfit_AP2Nef_021125.pdb
Chain information for bestfit_AP2Nef_021125.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
M | No description available
S | No description available
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/cryosparc_P24_J249_010_volume_map_sharp_resampled.mrc
Opened cryosparc_P24_J249_010_volume_map_sharp_resampled.mrc as #2, grid size
97,111,122, pixel 1.24,1.24,1.24, shown at level 2.47, step 1, values float32
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/cryosparc_P24_J250_volume_map_sharp_resampled.mrc
Opened cryosparc_P24_J250_volume_map_sharp_resampled.mrc as #3, grid size
97,111,122, pixel 1.24,1.24,1.24, shown at level 1.72, step 1, values float32
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/Phenixjobs/LocalAnisoSharpen_41/denmod_map_sharpened.ccp4
Opened denmod_map_sharpened.ccp4 as #4, grid size 97,111,122, pixel 1.24,
shown at level 3.91, step 1, values float32
> set bgColor white
> hide atoms
> show cartoons
> select add #1
23300 atoms, 23525 bonds, 1575 residues, 1 model selected
> ui tool show "Color Actions"
> color sel bychain
> select subtract #1
Nothing selected
> graphics silhouettes true
> lighting full
> volume #2 level 1.229
> close #3
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/cryosparc_P24_J249_010_volume_map_resampled.mrc
Opened cryosparc_P24_J249_010_volume_map_resampled.mrc as #3, grid size
97,111,122, pixel 1.24,1.24,1.24, shown at level 1.48, step 1, values float32
> volume #3 level 0.5866
> volume #3 color #b2b2ff7a
> volume #4 level 1.779
> surface dust #2 size 12.4
> surface dust #4 size 12.4
> surface dust #3 size 12.4
> volume #4 level 1.197
> volume #4 level 1.536
> volume #4 level 1.294
Cell requested for row 0 is out of bounds for table with 0 rows! Resizing
table model.
[Repeated 1 time(s)]
> select /C:81-210
2123 atoms, 2161 bonds, 130 residues, 1 model selected
Cell requested for row 0 is out of bounds for table with 0 rows! Resizing
table model.
> sequence chain #1/C
Alignment identifier is 1/C
Cell requested for row 0 is out of bounds for table with 0 rows! Resizing
table model.
[Repeated 1 time(s)]
> sequence chain #1/D
Alignment identifier is 1/D
Cell requested for row 0 is out of bounds for table with 0 rows! Resizing
table model.
> sequence chain #1/D
Destroying pre-existing alignment with identifier 1/D
Alignment identifier is 1/D
Cell requested for row 0 is out of bounds for table with 0 rows! Resizing
table model.
> select /D:1-2
31 atoms, 30 bonds, 2 residues, 1 model selected
> select /D
95 atoms, 94 bonds, 5 residues, 1 model selected
> ui tool show "Renumber Residues"
> renumber /D seqStart 15
5 residues renumbered
> renumber /C seqStart 109
130 residues renumbered
> ui tool show "Renumber Residues"
> help help:user/tools/renumber.html
> ui tool show "Change Chain IDs"
> changechains sel C,D N,N
Chain IDs of 5 residues changed
> changechains sel C N
No residues specified have any of the 'from' chain IDs
> ui tool show "Change Chain IDs"
> select /N:15-16
31 atoms, 30 bonds, 2 residues, 1 model selected
> select /N
95 atoms, 94 bonds, 5 residues, 1 model selected
> select /C:109-110
38 atoms, 38 bonds, 2 residues, 1 model selected
> select /C
2123 atoms, 2161 bonds, 130 residues, 1 model selected
> ui mousemode right select
> hide #!3 models
Drag select of 5 residues
> changechains sel N
Chain IDs of 130 residues changed
> select add #1
23300 atoms, 23525 bonds, 1575 residues, 1 model selected
Alignment identifier is 1/B
Alignment identifier is 1/A
Alignment identifier is 1/S
Alignment identifier is 1/M
Chains must have same sequence
> select #1/N
2218 atoms, 2255 bonds, 135 residues, 1 model selected
Chains must have same sequence
> close #1
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/bestfit_AP2Nef_021125.pdb
Chain information for bestfit_AP2Nef_021125.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
M | No description available
S | No description available
> hide atoms
> show cartoons
> show #!3 models
> hide #!2 models
> hide #!4 models
> show #!4 models
Drag select of 4 denmod_map_sharpened.ccp4 , 3
cryosparc_P24_J249_010_volume_map_resampled.mrc , 12 residues
> select clear
[Repeated 1 time(s)]
> ui mousemode right translate
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/side_view_extradensity.png
> width 1821 height 1179 supersample 2 transparentBackground true
> hide #!3 models
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/Serinc5Ap2Nef_project_02112025.cxs
> includeMaps true
——— End of log from Tue Feb 11 16:42:50 2025 ———
opened ChimeraX session
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> color #4 #b2ffff7f models
> color #4 #b2ffff80 models
> select add #1
23300 atoms, 23525 bonds, 1575 residues, 1 model selected
> ui tool show "Color Actions"
> color sel bychain
> hide #!4 models
> show #!4 models
> select subtract #1
Nothing selected
> volume #4 level 0.9439
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/joanapaulino/Desktop/movie38.mp4
Movie saved to /Users/joanapaulino/Desktop/movie38.mp4
> select clear
> select /D:5
25 atoms, 24 bonds, 1 residue, 1 model selected
> select ~sel
23275 atoms, 23500 bonds, 1574 residues, 7 models selected
> select down
23275 atoms, 23500 bonds, 1574 residues, 7 models selected
> select clear
> hide #!4 models
Drag select of 1 residues
Drag select of 5 residues
> show sel cartoons
> hide sel cartoons
> show #!4 models
> color #4 #b2ffff5f models
> color #4 #b2ffff5a models
> color #4 #d2fff55a models
> color #4 #d2fff559 models
> lighting shadows false
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/joanapaulino/Desktop/movie39.mp4
Movie saved to /Users/joanapaulino/Desktop/movie39.mp4
> select add #1
23300 atoms, 23525 bonds, 1575 residues, 1 model selected
> show sel surfaces
[Repeated 1 time(s)]
> select /D:5@NE
1 atom, 1 residue, 1 model selected
> select ~sel
23299 atoms, 23522 bonds, 1575 residues, 7 models selected
> select ~sel
1 atom, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 2 models selected
> select /D:1@HA
1 atom, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 2 models selected
> select /D:5@NH1
1 atom, 1 residue, 1 model selected
> select ~sel
23299 atoms, 23522 bonds, 1575 residues, 7 models selected
> select ~sel
1 atom, 1 residue, 1 model selected
> select ~sel
23299 atoms, 23522 bonds, 1575 residues, 7 models selected
> select ~sel
1 atom, 1 residue, 1 model selected
> hide #!4 models
> select /D:3@NH1
1 atom, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 1 residue, 2 models selected
> select up
95 atoms, 94 bonds, 5 residues, 2 models selected
> hide sel surfaces
> show #!4 models
> volume #4 level 0.6441
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/joanapaulino/Desktop/movie38.mp4
Movie saved to /Users/joanapaulino/Desktop/movie38.mp4
> show #!3 models
> hide #!4 models
> hide #!1 models
> volume #3 level 0.4184
> volume #3 level 0.5427
> show #!1 models
> volume #3 level 0.5939
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/joanapaulino/Desktop/movie38.mp4
Movie saved to /Users/joanapaulino/Desktop/movie38.mp4
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/cryosparc_P24_J221_volume_map_consensus.mrc
Opened cryosparc_P24_J221_volume_map_consensus.mrc as #5, grid size
144,144,144, pixel 2.86, shown at level 0.46, step 1, values float32
> ui tool show "Fit in Map"
> fitmap #5 inMap #2
Fit map cryosparc_P24_J221_volume_map_consensus.mrc in map
cryosparc_P24_J249_010_volume_map_sharp_resampled.mrc using 29853 points
correlation = 0.6993, correlation about mean = 0.5935, overlap = 2.418e+04
steps = 208, shift = 9.97, angle = 0.591 degrees
Position of cryosparc_P24_J221_volume_map_consensus.mrc (#5) relative to
cryosparc_P24_J249_010_volume_map_sharp_resampled.mrc (#2) coordinates:
Matrix rotation and translation
0.99994840 -0.00953936 0.00349179 -5.14621176
0.00953299 0.99995287 0.00183650 -7.91370651
-0.00350914 -0.00180312 0.99999222 -4.11791779
Axis -0.17633736 0.33919048 0.92404272
Axis point 628.33698722 -646.05332744 0.00000000
Rotation angle (degrees) 0.59130603
Shift along axis -5.58191648
> volume #5 level 0.7708
> volume #5 level 1.069
> hide #!3 models
> color #5 #ffb2ff86 models
> color #5 #ffb2ff85 models
> volume #5 level 0.9201
> volume #5 level 1.442
> show #!3 models
> hide #!3 models
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/Serinc5Ap2Nef_project_02252025.cxs
> includeMaps true
> hide #!5 models
> show sel cartoons
> hide sel surfaces
[Repeated 4 time(s)]
> select clear
> hide surfaces
> open "/Users/joanapaulino/Documents/postdoc_UCSF/Serinc/Nef_AP2
> structures/Nef_AP2_noTet.pdb"
Chain information for Nef_AP2_noTet.pdb #6
---
Chain | Description
A | No description available
B | No description available
M | No description available
N | No description available
S | No description available
> hide atoms
> show cartoons
> ui tool show Matchmaker
> matchmaker #!6 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker bestfit_AP2Nef_021125.pdb, chain A (#1) with Nef_AP2_noTet.pdb,
chain A (#6), sequence alignment score = 2903.7
RMSD between 217 pruned atom pairs is 0.912 angstroms; (across all 590 pairs:
5.521)
> matchmaker #!6 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker bestfit_AP2Nef_021125.pdb, chain A (#1) with Nef_AP2_noTet.pdb,
chain A (#6), sequence alignment score = 2903.7
RMSD between 217 pruned atom pairs is 0.912 angstroms; (across all 590 pairs:
5.521)
> select add #6
11575 atoms, 11796 bonds, 1 pseudobond, 1565 residues, 2 models selected
> color (#!6 & sel) dark gray
> select clear
> open "/Users/joanapaulino/Documents/postdoc_UCSF/Serinc/Nef_AP2
> structures/6owt.pdb"
6owt.pdb title:
Structure of sivsmm nef and SMM tetherin bound to the clathrin adaptor ap-2
complex [more info...]
Chain information for 6owt.pdb #7
---
Chain | Description | UniProt
A | ap-2 complex subunit α | Q66HM2_RAT 1-939
B | ap-2 complex subunit β | AP2B1_RAT 1-591
M | adaptor protein complex ap-2, Μ1 | Q5FWI9_MOUSE 1-141
N T | tetherin,protein nef | C3VHQ5_CERAT -32--12 -4-16, Q4JGV0_SIV 1-251 29-270
S | ap-2 complex subunit σ | AP2S1_RAT 1-142
> hide atoms
> show cartoons
> color #1,6-7 dark gray
> select add #1
23300 atoms, 23525 bonds, 1575 residues, 1 model selected
> ui tool show "Color Actions"
> color sel bychain
> select subtract #1
6 models selected
> ui tool show Matchmaker
> matchmaker #!7 to #6
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 Nef_AP2_noTet.pdb, chain A (#6) with 6owt.pdb, chain A (#7),
sequence alignment score = 3048
RMSD between 590 pruned atom pairs is 0.000 angstroms; (across all 590 pairs:
0.000)
> matchmaker #!7 to #6
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 Nef_AP2_noTet.pdb, chain A (#6) with 6owt.pdb, chain A (#7),
sequence alignment score = 3048
RMSD between 590 pruned atom pairs is 0.000 angstroms; (across all 590 pairs:
0.000)
> hide #!6 models
Cell requested for row 0 is out of bounds for table with 0 rows! Resizing
table model.
> select #7/T:3-12
74 atoms, 76 bonds, 10 residues, 1 model selected
Cell requested for row 0 is out of bounds for table with 0 rows! Resizing
table model.
> select #7/T:3-12
74 atoms, 76 bonds, 10 residues, 1 model selected
> color sel red
> select clear
> hide #!1 models
> show #!3 models
> show #!5 models
> hide #!3 models
> volume #5 level 1.355
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> show #!3 models
> show #!7 models
> hide #!6 models
> hide #!5 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!4 models
> hide #!3 models
> hide #!4 models
> hide #!7 models
> show #!1 models
> select #1A
Expected an objects specifier or a keyword
> select #1/a
8890 atoms, 8968 bonds, 612 residues, 1 model selected
> select #1/A:11,43,57,58,61
111 atoms, 108 bonds, 5 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 111 atom styles
> select clear
> select #1/A:11,43,57,58,61
111 atoms, 108 bonds, 5 residues, 1 model selected
> color (#!1 & sel) byhetero
> select clear
> show #!4 models
> hide #!4 models
> show #!5 models
> volume #5 level 0.8703
> volume #5 level 0.7957
> volume #5 level 0.7708
> volume #5 level 0.9076
> volume #5 level 1.343
> volume #5 level 1.728
> show #!3 models
> hide #!5 models
> volume #3 level 0.9156
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/Serinc5Ap2Nef_project_02252025.cxs
> includeMaps true
——— End of log from Tue Feb 25 18:08:00 2025 ———
opened ChimeraX session
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/bestfit_AP2Nef_030225_Nef.pdb
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/bestfit_AP2Nef_030225_chainS.pdb
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/bestfit_AP2Nef_030225_chainM.pdb
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/bestfit_AP2Nef_030225_chainD.pdb
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/bestfit_AP2Nef_030225_chainC.pdb
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/bestfit_AP2Nef_030225_chainB.pdb
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/bestfit_AP2Nef_030225_chainA.pdb
Summary of feedback from opening
/Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/bestfit_AP2Nef_030225_Nef.pdb
---
warnings | Ignored bad PDB record found on line 115
PDB SEQRES record for chain N is incomplete. Ignoring input sequence records
as basis for sequence.
Chain information for bestfit_AP2Nef_030225_Nef.pdb #8
---
Chain | Description
N | No description available
Chain information for bestfit_AP2Nef_030225_chainS.pdb #9
---
Chain | Description
S | No description available
Chain information for bestfit_AP2Nef_030225_chainM.pdb #10
---
Chain | Description
M | No description available
Chain information for bestfit_AP2Nef_030225_chainD.pdb #11
---
Chain | Description
D | No description available
Chain information for bestfit_AP2Nef_030225_chainC.pdb #12
---
Chain | Description
C | No description available
Chain information for bestfit_AP2Nef_030225_chainB.pdb #13
---
Chain | Description
B | No description available
Chain information for bestfit_AP2Nef_030225_chainA.pdb #14
---
Chain | Description
A | No description available
> hide #!1 models
> hide #9-14#!8 atoms
> close #11
> close #12
> combine #14,#13,#10,#9,#8
Expected a keyword
> combine #14 #13 #10 #9 #8
> hide #!3 models
> show #!3 models
> hide #!8 models
> hide #9 models
> hide #!11 models
> hide #13 models
> hide #14 models
> hide #10 models
> show #!11 models
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/bestfit_AP2Nef_03032025.pdb
> models #11
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/bestfit_AP2Nef_03032025.pdb
Chain information for bestfit_AP2Nef_03032025.pdb #12
---
Chain | Description
A | No description available
B | No description available
M | No description available
N | No description available
S | No description available
> hide #!11-12 atoms
> show #!11-12 cartoons
> close #1
> close #8
> close #9
> close #10
> close #13
> close #14
> hide #!11 models
> hide #!12 models
> show #!11 models
> show #!12 models
> hide #!11 models
> close #11
> select add #12
23313 atoms, 23539 bonds, 1 pseudobond, 1575 residues, 2 models selected
> ui tool show "Color Actions"
> color sel bychain
> select subtract #12
Nothing selected
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/Serinc5Ap2Nef_project_maps_models_03032025.cxs
> includeMaps true
——— End of log from Sun Mar 2 22:52:36 2025 ———
opened ChimeraX session
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/Docking_MD_Serinc5_AP2Nef/cluster2_1.pdb
Summary of feedback from opening
/Users/joanapaulino/Documents/postdoc_UCSF/Serinc/Docking_MD_Serinc5_AP2Nef/cluster2_1.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK FILENAME="complex_119w.pdb0"
Ignored bad PDB record found on line 2
REMARK ===============================================================
Ignored bad PDB record found on line 3
REMARK HADDOCK run for complex
Ignored bad PDB record found on line 4
REMARK initial structure: complex_119.pdb
Ignored bad PDB record found on line 5
REMARK ===============================================================
29 messages similar to the above omitted
Chain information for cluster2_1.pdb #1
---
Chain | Description
A | No description available
B | No description available
> ui tool show Matchmaker
> matchmaker #1 to #12
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 bestfit_AP2Nef_03032025.pdb, chain S (#12) with cluster2_1.pdb,
chain A (#1), sequence alignment score = 720.1
RMSD between 140 pruned atom pairs is 0.530 angstroms; (across all 140 pairs:
0.530)
> hide #!12 models
> select #1/A:1-140
1442 atoms, 1466 bonds, 140 residues, 1 model selected
> select #1/A:1-140
1442 atoms, 1466 bonds, 140 residues, 1 model selected
> select #1/A:1-140
1442 atoms, 1466 bonds, 140 residues, 1 model selected
> color sel red
> volume #3 level 0.3891
> volume #3 level 0.9887
> select #1/A:1-140
1442 atoms, 1466 bonds, 140 residues, 1 model selected
> select #1/A:1-140
1442 atoms, 1466 bonds, 140 residues, 1 model selected
> select #1/A:1-140
1442 atoms, 1466 bonds, 140 residues, 1 model selected
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #1/A
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
> select add #1
5971 atoms, 6096 bonds, 620 residues, 1 model selected
> select subtract #1
Nothing selected
> show #!2 models
> volume #2 level 0.4878
> volume #2 level 1.314
> hide #!2 models
> show #!4 models
> hide #!3 models
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> volume #4 level 2.093
> volume #4 level 1.743
> hide #!4 models
> show #!5 models
> volume #5 level 0.7335
> show #!3 models
> hide #!3 models
> hide #!5 models
> show #!6 models
> show #!5 models
> hide #!6 models
> hide #1 models
> volume #5 level 0.6838
> show #1 models
> show #!12 models
> hide #!5 models
> show #!3 models
> volume #3 level 0.3599
> volume #3 level 0.762
> show #!5 models
> volume #5 level 0.7957
> volume #5 level 0.7584
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/Serinc5Ap2Nef_project_maps_withdocking_04172025.cxs
> includeMaps true
——— End of log from Thu Apr 17 14:19:45 2025 ———
opened ChimeraX session
> hide #1 models
> hide #!5 models
> hide #!3 models
> show #!2 models
> volume #2 level 0.7331
> volume #2 color #7b7b7b
> volume #2 color #b9b9b9
> volume #2 color #b9b9b97b
> color #2 #8279bfff models
> color #2 #5d5fbfff models
> color #2 #7883bfff models
> color #2 #7883bf78 models
> color #2 #cbc5bd78 models
> set bgColor black
> color #2 #c8c9cb78 models
> color #2 #c8c9cb8b models
> show #1 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!2 models
> set bgColor white
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> close #7
> close #3
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/cryosparc_P27_J86_004_volume_map.mrc
Opened cryosparc_P27_J86_004_volume_map.mrc as #3, grid size 256,256,256,
pixel 1.33, shown at level 0.127, step 1, values float32
> ui mousemode right select
> ui mousemode right "translate selected models"
> select add #3
2 models selected
> view matrix models #3,1,0,0,-49.213,0,1,0,-29.446,0,0,1,4.6433
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.49798,-0.828,-0.25776,390.13,-0.86659,0.46408,0.18345,180.28,-0.032273,0.31473,-0.94863,273.72
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.49798,-0.828,-0.25776,471.73,-0.86659,0.46408,0.18345,224,-0.032273,0.31473,-0.94863,295.87
> view matrix models
> #3,-0.49798,-0.828,-0.25776,473.5,-0.86659,0.46408,0.18345,229.8,-0.032273,0.31473,-0.94863,295.04
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.87326,-0.34966,-0.33934,467.95,-0.40204,0.91053,0.096388,88.05,0.27528,0.2206,-0.93571,256.96
> ui tool show "Fit in Map"
> fitmap #3 inMap #4
Fit map cryosparc_P27_J86_004_volume_map.mrc in map denmod_map_sharpened.ccp4
using 167620 points
correlation = 0.3425, correlation about mean = 0.3108, overlap = 3.448e+04
steps = 196, shift = 14, angle = 25 degrees
Position of cryosparc_P27_J86_004_volume_map.mrc (#3) relative to
denmod_map_sharpened.ccp4 (#4) coordinates:
Matrix rotation and translation
-0.96346586 -0.25771906 0.07289920 391.25575931
-0.24462869 0.95759087 0.15223816 51.68881411
-0.10904228 0.12884304 -0.98565162 356.98165676
Axis -0.12721247 0.98931817 0.07117973
Axis point 207.21932702 0.00000000 167.44136265
Rotation angle (degrees) 174.72402992
Shift along axis 26.77392845
> color #3 #bf912aff models
> color #3 #bf912a83 models
> color #3 #bf912a82 models
> color #4 #d2fff5ff models
> ui mousemode right select
> select clear
> color #3 #c0a3cb82 models
> volume #3 level 0.1098
> hide #1 models
> volume #4 level 0.7217
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/cryosparc_P27_J169_006_volume_map_sharp.mrc
Opened cryosparc_P27_J169_006_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 1.33, shown at level 0.159, step 1, values float32
> surface dust #4 size 12.4
> surface dust #3 size 13.3
> surface dust #7 size 13.3
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> fitmap #7 inMap #4
Fit map cryosparc_P27_J169_006_volume_map_sharp.mrc in map
denmod_map_sharpened.ccp4 using 166885 points
correlation = 0.06151, correlation about mean = 0.01585, overlap = 7667
steps = 1272, shift = 23.2, angle = 26.1 degrees
Position of cryosparc_P27_J169_006_volume_map_sharp.mrc (#7) relative to
denmod_map_sharpened.ccp4 (#4) coordinates:
Matrix rotation and translation
0.93221597 0.34573317 0.10696713 -52.27512127
-0.30530050 0.90999317 -0.28054241 128.56452027
-0.19433218 0.22886899 0.95386267 10.71782266
Axis 0.57897899 0.34244615 -0.73994186
Axis point 347.05485705 229.00652377 -0.00000000
Rotation angle (degrees) 26.09891589
Shift along axis 5.82966208
> fitmap #7 inMap #4
Fit map cryosparc_P27_J169_006_volume_map_sharp.mrc in map
denmod_map_sharpened.ccp4 using 166885 points
correlation = 0.06151, correlation about mean = 0.01585, overlap = 7667
steps = 44, shift = 0.0043, angle = 0.0047 degrees
Position of cryosparc_P27_J169_006_volume_map_sharp.mrc (#7) relative to
denmod_map_sharpened.ccp4 (#4) coordinates:
Matrix rotation and translation
0.93222485 0.34568859 0.10703374 -52.27990730
-0.30523991 0.91001126 -0.28054965 128.54828464
-0.19438473 0.22886439 0.95385307 10.73026552
Axis 0.57900534 0.34259540 -0.73985215
Axis point 347.06823586 229.04611214 0.00000000
Rotation angle (degrees) 26.09778413
Shift along axis 5.83089479
> select add #7
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.84486,0.50163,0.18594,198.87,0.45868,0.85809,-0.23086,4.1683,-0.27536,-0.10976,-0.95506,397.67
> fitmap #7 inMap #4
Fit map cryosparc_P27_J169_006_volume_map_sharp.mrc in map
denmod_map_sharpened.ccp4 using 166885 points
correlation = 0.0594, correlation about mean = 0.01871, overlap = 7496
steps = 188, shift = 5.65, angle = 5.88 degrees
Position of cryosparc_P27_J169_006_volume_map_sharp.mrc (#7) relative to
denmod_map_sharpened.ccp4 (#4) coordinates:
Matrix rotation and translation
-0.86231574 0.49040453 0.12615453 219.28647055
0.43602383 0.84578589 -0.30745642 21.97255882
-0.25747774 -0.21011813 -0.94316254 410.05363265
Axis 0.24364611 0.96026457 -0.13611957
Axis point 128.53133958 0.00000000 195.30361365
Rotation angle (degrees) 168.47745940
Shift along axis 18.71144284
> hide #!3 models
> fitmap #7 inMap #4
Fit map cryosparc_P27_J169_006_volume_map_sharp.mrc in map
denmod_map_sharpened.ccp4 using 166885 points
correlation = 0.0594, correlation about mean = 0.0187, overlap = 7496
steps = 52, shift = 0.0135, angle = 0.00384 degrees
Position of cryosparc_P27_J169_006_volume_map_sharp.mrc (#7) relative to
denmod_map_sharpened.ccp4 (#4) coordinates:
Matrix rotation and translation
-0.86230764 0.49042195 0.12614213 219.27908285
0.43602666 0.84576183 -0.30751858 21.99882737
-0.25750006 -0.21017429 -0.94314393 410.06109767
Axis 0.24365321 0.96025821 -0.13615168
Axis point 128.52557476 0.00000000 195.30966937
Rotation angle (degrees) 168.47708031
Shift along axis 18.72210149
> fitmap #7 inMap #4
Fit map cryosparc_P27_J169_006_volume_map_sharp.mrc in map
denmod_map_sharpened.ccp4 using 166885 points
correlation = 0.05939, correlation about mean = 0.01871, overlap = 7495
steps = 44, shift = 0.00804, angle = 0.00434 degrees
Position of cryosparc_P27_J169_006_volume_map_sharp.mrc (#7) relative to
denmod_map_sharpened.ccp4 (#4) coordinates:
Matrix rotation and translation
-0.86228520 0.49047103 0.12610473 219.27714779
0.43609056 0.84573900 -0.30749075 21.98402640
-0.25746699 -0.21015164 -0.94315801 410.05990816
Axis 0.24368352 0.96025236 -0.13613873
Axis point 128.52222951 0.00000000 195.30995951
Rotation angle (degrees) 168.47915493
Shift along axis 18.71940442
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.86229,0.49047,0.1261,219.51,0.43609,0.84574,-0.30749,84.181,-0.25747,-0.21015,-0.94316,411.22
> volume #7 level 0.3677
> view matrix models
> #7,-0.86229,0.49047,0.1261,220.11,0.43609,0.84574,-0.30749,41.584,-0.25747,-0.21015,-0.94316,429.72
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.44955,0.8812,0.14625,82.208,0.88717,0.4214,0.188,-52.316,0.10403,0.21427,-0.97122,303.45
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.44955,0.8812,0.14625,98.647,0.88717,0.4214,0.188,-58.525,0.10403,0.21427,-0.97122,309.96
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.98035,-0.18708,0.062535,381.95,-0.18148,0.97965,0.08569,43.074,-0.077293,0.072658,-0.99436,368.09
> fitmap #7 inMap #4
Fit map cryosparc_P27_J169_006_volume_map_sharp.mrc in map
denmod_map_sharpened.ccp4 using 59750 points
correlation = 0.8166, correlation about mean = 0.7146, overlap = 1.302e+05
steps = 196, shift = 9.02, angle = 4.99 degrees
Position of cryosparc_P27_J169_006_volume_map_sharp.mrc (#7) relative to
denmod_map_sharpened.ccp4 (#4) coordinates:
Matrix rotation and translation
-0.96337451 -0.26143316 0.05968457 394.25444951
-0.25198447 0.95868843 0.13198598 56.27998048
-0.09172442 0.11211235 -0.98945310 357.10416222
Axis -0.12989327 0.98960291 0.06175621
Axis point 207.70059055 0.00000000 169.09878686
Rotation angle (degrees) 175.61259380
Shift along axis 26.53723447
> hide #!4 models
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/Phenixjobs/LocalAnisoSharpen_50/denmod_map_sharpened.ccp4
Opened denmod_map_sharpened.ccp4 as #8, grid size 256,256,256, pixel 1.33,
shown at level 0.0194, step 1, values float32
> surface dust #7 size 13.3
[Repeated 1 time(s)]
> ui mousemode right select
> select clear
> surface dust #7 size 13.3
> surface dust #8 size 13.3
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> select add #8
2 models selected
> view matrix models
> #8,-0.99502,-0.022188,-0.097177,349.75,-0.0058498,0.98623,-0.16528,32.958,0.099506,-0.16389,-0.98145,366.97
> volume #8 level 0.06246
> volume #8 level 0.0883
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.99502,-0.022188,-0.097177,384.28,-0.0058498,0.98623,-0.16528,62.051,0.099506,-0.16389,-0.98145,363.47
> fitmap #8 inMap #4
Fit map denmod_map_sharpened.ccp4 in map denmod_map_sharpened.ccp4 using 42839
points
correlation = 0.169, correlation about mean = 0.04852, overlap = 5061
steps = 84, shift = 8.1, angle = 9.11 degrees
Position of denmod_map_sharpened.ccp4 (#8) relative to
denmod_map_sharpened.ccp4 (#4) coordinates:
Matrix rotation and translation
-0.99881070 -0.04655374 -0.01448952 372.17981273
-0.04602945 0.99833973 -0.03462776 47.87384321
0.01607752 -0.03391963 -0.99929524 365.18154099
Axis 0.02315677 -0.99958482 0.01714496
Axis point 185.24572029 0.00000000 184.42757812
Rotation angle (degrees) 179.12392082
Shift along axis -32.97446086
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.9239,-0.37984,0.046241,405.37,-0.37534,0.92312,0.083433,93.157,-0.074377,0.059727,-0.99544,363.43
> fitmap #8 inMap #4
Fit map denmod_map_sharpened.ccp4 in map denmod_map_sharpened.ccp4 using 42839
points
correlation = 0.8488, correlation about mean = 0.7106, overlap = 3.92e+04
steps = 120, shift = 5.05, angle = 8.21 degrees
Position of denmod_map_sharpened.ccp4 (#8) relative to
denmod_map_sharpened.ccp4 (#4) coordinates:
Matrix rotation and translation
-0.96355072 -0.26040696 0.06130437 393.94566458
-0.24975150 0.95772978 0.14275108 53.27419604
-0.09588639 0.12223705 -0.98785825 355.03080297
Axis -0.12911538 0.98935910 0.06706551
Axis point 207.55258024 0.00000000 167.72266940
Rotation angle (degrees) 175.44358218
Shift along axis 25.65319127
> hide #!7 models
> show #!4 models
> color #4 #fe3128ff models
> fitmap #8 inMap #4
Fit map denmod_map_sharpened.ccp4 in map denmod_map_sharpened.ccp4 using 42839
points
correlation = 0.8488, correlation about mean = 0.7107, overlap = 3.92e+04
steps = 48, shift = 0.0274, angle = 0.0216 degrees
Position of denmod_map_sharpened.ccp4 (#8) relative to
denmod_map_sharpened.ccp4 (#4) coordinates:
Matrix rotation and translation
-0.96356137 -0.26035520 0.06135683 393.93364244
-0.24972937 0.95779041 0.14238253 53.33863345
-0.09583702 0.12187170 -0.98790818 355.06800208
Axis -0.12909468 0.98937445 0.06687874
Axis point 207.55091153 0.00000000 167.74446357
Rotation angle (degrees) 175.44356318
Shift along axis 25.66364347
> ui mousemode right select
> select clear
> volume #8 level 0.06196
> select clear
> ui mousemode right translate
> volume #4 level 0.3733
> hide #!4 models
> show #!4 models
> hide #!8 models
> show #!8 models
> hide #!4 models
> show #!7 models
> volume #7 level 0.2873
> hide #!7 models
> hide #!8 models
> show #1 models
> hide #1 models
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/refit_AP2Nef_rigid_body_081325.pdb
Chain information for refit_AP2Nef_rigid_body_081325.pdb #9
---
Chain | Description
A | No description available
B | No description available
M | No description available
N | No description available
S | No description available
> hide #!9,12 atoms
> show #!9,12 cartoons
> ui tool show Matchmaker
> matchmaker #!9 to #12
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 bestfit_AP2Nef_03032025.pdb, chain A (#12) with
refit_AP2Nef_rigid_body_081325.pdb, chain A (#9), sequence alignment score =
3131.6
RMSD between 612 pruned atom pairs is 0.621 angstroms; (across all 612 pairs:
0.621)
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/cryosparc_P27_J141_flex_map.mrc
Opened cryosparc_P27_J141_flex_map.mrc as #10, grid size 256,256,256, pixel
1.33, shown at level 0.00547, step 1, values float32
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> select add #12
23313 atoms, 23539 bonds, 1 pseudobond, 1575 residues, 2 models selected
> select subtract #12
Nothing selected
> select add #10
2 models selected
> view matrix models
> #10,-0.39019,-0.69891,-0.5994,455.04,-0.9207,0.30185,0.24738,242.94,0.0080308,0.64839,-0.76126,157.38
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.39019,-0.69891,-0.5994,460.98,-0.9207,0.30185,0.24738,235.81,0.0080308,0.64839,-0.76126,185.1
> fitmap #10 inMap #3
Fit map cryosparc_P27_J141_flex_map.mrc in map
cryosparc_P27_J86_004_volume_map.mrc using 167754 points
correlation = 0.5481, correlation about mean = 0.08194, overlap = 363
steps = 536, shift = 44, angle = 55.7 degrees
Position of cryosparc_P27_J141_flex_map.mrc (#10) relative to
cryosparc_P27_J86_004_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.86304810 -0.29729772 0.40836522 5.51564204
-0.27539802 0.40077578 0.87380478 6.33841640
-0.42344303 -0.86659850 0.26401355 367.07140409
Axis -0.90218875 0.43119204 0.01135235
Axis point 0.00000000 271.04666949 179.56980595
Rotation angle (degrees) 74.69728821
Shift along axis 1.92404664
> show #!3 models
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.68737,0.69846,-0.19918,-5.8329,0.71705,-0.69623,0.033076,202.28,-0.11557,-0.16555,-0.97941,386.95
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.68737,0.69846,-0.19918,-9.1264,0.71705,-0.69623,0.033076,205.6,-0.11557,-0.16555,-0.97941,412.77
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.97629,0.035855,-0.21348,393.65,-0.017714,0.96965,0.24387,-5.6057,0.21574,0.24187,-0.94602,277.84
> fitmap #10 inMap #3
Fit map cryosparc_P27_J141_flex_map.mrc in map
cryosparc_P27_J86_004_volume_map.mrc using 167754 points
correlation = 0.9937, correlation about mean = 0.969, overlap = 920
steps = 196, shift = 2.31, angle = 24.1 degrees
Position of cryosparc_P27_J141_flex_map.mrc (#10) relative to
cryosparc_P27_J86_004_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99998432 0.00265206 0.00494389 -1.40155691
-0.00263801 0.99999252 -0.00284351 0.99648980
-0.00495139 0.00283041 0.99998379 0.32244093
Axis 0.45125783 0.78699004 -0.42072918
Axis point 65.55297294 0.00000000 285.17160653
Rotation angle (degrees) 0.36020857
Shift along axis 0.01610372
> select subtract #10
Nothing selected
> show #1 models
> select add #1
5971 atoms, 6096 bonds, 620 residues, 1 model selected
> hide #!9 models
> show #!9 models
> hide #!10 models
> hide #!12 models
> ui mousemode right "rotate selected models"
> ui mousemode right select
> hide #1 models
> show #1 models
> hide #1 models
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/alphafold_predictions/fold_2025_02_09_18_49_serinc5/fold_2025_02_09_18_49_serinc5_model_4.cif
Chain information for fold_2025_02_09_18_49_serinc5_model_4.cif #11
---
Chain | Description
A | .
> show #11#!9 cartoons
[Repeated 2 time(s)]
> select add #11
9719 atoms, 9945 bonds, 1100 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.072227,0.96932,0.23494,262.17,0.16703,-0.22048,0.96098,352.3,0.9833,0.10865,-0.14598,470.88,#11,1,0,0,59.169,0,1,0,154.38,0,0,1,236.3
> view matrix models
> #1,-0.072227,0.96932,0.23494,391.72,0.16703,-0.22048,0.96098,443.1,0.9833,0.10865,-0.14598,526.47,#11,1,0,0,188.72,0,1,0,245.17,0,0,1,291.89
> ui mousemode right translate
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.80621,0.57075,0.15578,119.41,-0.58388,-0.72509,-0.36515,-102.88,-0.095455,-0.38535,0.91782,379.66,#11,0.64807,-0.11079,-0.75348,186.53,-0.74646,-0.28857,-0.5996,246.42,-0.151,0.95103,-0.26972,285.36
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.80621,0.57075,0.15578,114.65,-0.58388,-0.72509,-0.36515,-129.4,-0.095455,-0.38535,0.91782,347.45,#11,0.64807,-0.11079,-0.75348,181.76,-0.74646,-0.28857,-0.5996,219.9,-0.151,0.95103,-0.26972,253.14
> view matrix models
> #1,-0.80621,0.57075,0.15578,123.41,-0.58388,-0.72509,-0.36515,-131.23,-0.095455,-0.38535,0.91782,346.71,#11,0.64807,-0.11079,-0.75348,190.53,-0.74646,-0.28857,-0.5996,218.07,-0.151,0.95103,-0.26972,252.4
> view matrix models
> #1,-0.80621,0.57075,0.15578,122.75,-0.58388,-0.72509,-0.36515,-132.19,-0.095455,-0.38535,0.91782,342.65,#11,0.64807,-0.11079,-0.75348,189.87,-0.74646,-0.28857,-0.5996,217.11,-0.151,0.95103,-0.26972,248.34
> ui mousemode right select
> select clear
> color #11 #4c5ba7ff
> hide #!9 models
> hide #11 models
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/comparison_processing_2024_2025.cxs
> includeMaps true
——— End of log from Mon Aug 18 17:27:18 2025 ———
opened ChimeraX session
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!9 models
> volume #5 level 0.8454
> hide #!5 models
> volume #3 level 0.1124
> show #11 models
> volume #3 level 0.1098
> color #3 #c0a3cbc8 models
> color #3 #c0a3cbb3 models
> select #9/N
2218 atoms, 2255 bonds, 1 pseudobond, 135 residues, 2 models selected
> color #9 #29b5c4ff
> color #9 #32ddf0ff
> graphics silhouettes false
> graphics silhouettes true
> select #9/B
8235 atoms, 8301 bonds, 564 residues, 1 model selected
> color sel red
> select #9/A
8924 atoms, 9002 bonds, 612 residues, 1 model selected
> color sel magenta
> select #9/S
2218 atoms, 2242 bonds, 140 residues, 1 model selected
> color sel orange
> select #9/M
1839 atoms, 1860 bonds, 124 residues, 1 model selected
> color sel lime
> ui mousemode right select
> select clear
> volume #3 color #c0a3cb92
> volume #3 color #c0a3cb91
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/CSp27_j86_structureoverlay.png
> width 1528 height 804 supersample 1 transparentBackground true
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> show #!7 models
> volume #7 level 0.2603
> volume #7 level 0.3815
> hide #!7 models
> show #!8 models
> volume #8 level 0.1043
> hide #11 models
> show #11 models
> hide #11 models
> show #!10 models
> hide #!10 models
> show #!7 models
> hide #!8 models
> volume #7 level 0.4757
> hide #!7 models
> show #!4 models
> volume #4 level 1.322
> volume #4 level 1.223
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!8 models
> volume #8 level 0.0884
> hide #!9 models
> show #!7 models
> volume #7 level 0.4891
> hide #!8 models
> show #!9 models
> volume #7 level 0.4084
> show #!4 models
> hide #!7 models
> hide #!4 models
> show #!8 models
> hide #!8 models
> show #!7 models
> volume #7 level 0.7313
> show #!2 models
> hide #!7 models
> show #11 models
> volume #2 level 0.6761
> volume #2 level 1.075
> show #!7 models
> volume #7 level 0.516
> hide #!7 models
> volume #2 level 0.7616
> show #!4 models
> hide #!2 models
> color #4 #acffd8ff models
> color #4 #acffd877 models
> color #4 #acffd878 models
> volume #4 level 1.372
> hide #!4 models
> show #!2 models
> volume #2 level 1.816
> hide #!2 models
> show #!8 models
> volume #8 level 0.1148
> color #8 #b2ffff81 models
> color #8 #b2ffff82 models
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/comparison_processing_2024_2025.cxs
> includeMaps true
——— End of log from Thu Sep 18 21:45:21 2025 ———
opened ChimeraX session
> hide #!8 models
> hide #!9 models
> hide #11 models
> show #!2 models
> color #2 #c8c9cbff models
> volume #2 level 1.246
> volume #2 level 1.047
> volume #2 level 0.9896
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/cs_p24_j249_resampled_sharp.png
> width 1026 height 858 supersample 1 transparentBackground true
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/bestfit_AP2nef_08122025.pdb
Chain information for bestfit_AP2nef_08122025.pdb #13
---
Chain | Description
A | No description available
B | No description available
M | No description available
N | No description available
S | No description available
> hide #!13 atoms
> show #!13 cartoons
> ui tool show Matchmaker
> matchmaker #!13 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker refit_AP2Nef_rigid_body_081325.pdb, chain A (#9) with
bestfit_AP2nef_08122025.pdb, chain A (#13), sequence alignment score = 3150.8
RMSD between 612 pruned atom pairs is 0.591 angstroms; (across all 612 pairs:
0.591)
> color #2 #c8c9cb85 models
> select #13?a
Expected an objects specifier or a keyword
> select #13/A
8924 atoms, 9002 bonds, 612 residues, 1 model selected
> color sel blue
> color sel cyan
> select #13/B
8188 atoms, 8254 bonds, 564 residues, 1 model selected
> ui tool show "Color Actions"
> color sel chartreuse
> select #13/N
2218 atoms, 2255 bonds, 1 pseudobond, 135 residues, 2 models selected
> ui tool show "Color Actions"
> color sel yellow
> select #13/S
2218 atoms, 2242 bonds, 140 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light coral
> select #13/M
1839 atoms, 1860 bonds, 124 residues, 1 model selected
> color sel magenta
> hide #!13 models
> volume #2 level 0.8471
> color #2 #c8c9cbff models
> volume #2 level 0.9041
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/cs_p24_j249_resampled_sharp.png
> width 1026 height 858 supersample 1 transparentBackground true
> show #!13 models
> hide #!13 models
> show #!13 models
> color #2 #c8c9cb7b models
> color #2 #c8c9cb7a models
> volume #2 level 0.8471
> select add #13
23387 atoms, 23613 bonds, 1 pseudobond, 1575 residues, 2 models selected
> select subtract #13
Nothing selected
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/cs_p24_j249_resampled_sharp_with_model.png
> width 1026 height 858 supersample 1 transparentBackground true
> hide #!2 models
> show #!3 models
> hide #!13 models
> hide #!3 models
> show #!5 models
> volume #5 level 0.6962
> hide #!5 models
> show #!3 models
> volume #3 level 0.1278
> show #!5 models
> volume #3 level 0.1073
> hide #!5 models
> show #!10 models
> hide #!10 models
> show #!5 models
> hide #!3 models
> hide #!5 models
> show #!3 models
> volume #3 level 0.1021
> show #!13 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #11 models
> hide #11 models
> hide #!13 models
> show #!5 models
> hide #!3 models
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/cs_p24_j221_consensus_map.png
> width 1026 height 858 supersample 1 transparentBackground true
> hide #!5 models
> show #!3 models
> ui tool show "Map Eraser"
> volume erase #3 center 211.62,245.62,252.37 radius 13.3
> volume erase #3 center 227.63,226.57,251.49 radius 13.3
> volume erase #3 center 225.83,225.34,258.13 radius 13.3
> volume erase #3 center 217.71,207.29,267.53 radius 13.3
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/cs_p27_j86_refined_vol.png
> width 1026 height 858 supersample 1 transparentBackground true
> show #!13 models
> show #11 models
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/cs_p27_j86_refined_vol_overlay_map.png
> width 1026 height 858 supersample 1 transparentBackground true
> hide #!3 models
> hide #11 models
> open "/Users/joanapaulino/Documents/postdoc_UCSF/Serinc/Nef_AP2
> structures/Nef_AP2_noTet.pdb"
Chain information for Nef_AP2_noTet.pdb #14
---
Chain | Description
A | No description available
B | No description available
M | No description available
N | No description available
S | No description available
> hide #!13-14 atoms
> show #!13-14 cartoons
> ui tool show Matchmaker
> matchmaker #!14 to #13
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 bestfit_AP2nef_08122025.pdb, chain A (#13) with Nef_AP2_noTet.pdb,
chain A (#14), sequence alignment score = 2886.3
RMSD between 275 pruned atom pairs is 1.074 angstroms; (across all 590 pairs:
5.445)
> matchmaker #!14 to #13
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 bestfit_AP2nef_08122025.pdb, chain A (#13) with Nef_AP2_noTet.pdb,
chain A (#14), sequence alignment score = 2886.3
RMSD between 275 pruned atom pairs is 1.074 angstroms; (across all 590 pairs:
5.445)
> show #!12 models
> hide #!13 models
> show #!13 models
> hide #!12 models
> hide #!13 models
> show #!7 models
> hide #!14 models
> color #7 #ffffb282 models
> graphics silhouettes false
> graphics silhouettes true
> show #!2 models
> show #!13 models
> hide #!7 models
> show #!13 surfaces
> hide #!13 surfaces
> show #!13 atoms
> show #!7 models
> volume #7 level 0.3815
> hide #!7 models
> hide #!2 models
> show #!2 models
> show #!7 models
> hide #!2 models
> volume #7 level 0.6237
> hide #!7 models
> show #!2 models
> hide #!13 atoms
> hide #!13 cartoons
> show #!13 surfaces
> color #2 #c8c9cbff models
> color #2 #c8c9cb9c models
> color #2 #c8c9cba3 models
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/cs_p24_j249_resampled_sharp_with_modelvolume.png
> width 1026 height 858 supersample 1 transparentBackground true
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/cs_p24_j249_resampled_sharp_with_modelvolume_zoom.png
> width 1026 height 858 supersample 1 transparentBackground true
> select #13/S:97,99
22 atoms, 20 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 22 atom styles
> style sel stick
Changed 22 atom styles
> transparency sel 50
> style sel sphere
Changed 22 atom styles
> style sel sphere
Changed 22 atom styles
> transparency sel 0
> transparency sel 50
> transparency sel 0
> transparency sel 50
> transparency sel 0
> transparency sel 50
> style sel ball
Changed 22 atom styles
> ui tool show "Color Actions"
> color sel red
> color sel byelement
> select add #13
23387 atoms, 23613 bonds, 1 pseudobond, 1575 residues, 3 models selected
> select subtract #13
5 models selected
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/cs_p24_j249_resampled_sharp_with_modelvolume_zoom_topview_cys.png
> width 1026 height 858 supersample 3
> hide #!2 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
Alignment identifier is 4
Alignment identifier is 5
Alignment identifier is 6
Alignment identifier is 7
Alignment identifier is 8
Alignment identifier is 9
Alignment identifier is 10
> select #6/S:1-45 #14/S:1-45
708 atoms, 718 bonds, 90 residues, 2 models selected
> select #6/S:1-45 #14/S:1-45
708 atoms, 718 bonds, 90 residues, 2 models selected
5 [ID: 5] region 2 chains [1-45] RMSD: 1.019
> ui tool show "Model Panel"
> select add #14
11929 atoms, 12155 bonds, 1 pseudobond, 1610 residues, 3 models selected
> select subtract #14
354 atoms, 359 bonds, 45 residues, 1 model selected
> select add #13
23741 atoms, 23972 bonds, 1 pseudobond, 1620 residues, 3 models selected
> select subtract #13
354 atoms, 359 bonds, 45 residues, 6 models selected
> select add #13
23741 atoms, 23972 bonds, 1 pseudobond, 1620 residues, 3 models selected
> select add #6
34962 atoms, 35409 bonds, 2 pseudobonds, 3140 residues, 9 models selected
> select subtract #6
23387 atoms, 23613 bonds, 1 pseudobond, 1575 residues, 7 models selected
Alignment identifier is 13/A
Alignment identifier is 13/B
Alignment identifier is 13/M
Alignment identifier is 13/S
Alignment identifier is 13/N
> select #13/S:68
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #13/S:68-69
30 atoms, 29 bonds, 2 residues, 1 model selected
> select #13/S:70-71
27 atoms, 26 bonds, 2 residues, 1 model selected
> select #13/S:69-71
46 atoms, 45 bonds, 3 residues, 1 model selected
> select #13/S:4-9,14-19,58-62,65-69
420 atoms, 423 bonds, 22 residues, 1 model selected
> select #13/S:68
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #13/S:68-71
57 atoms, 56 bonds, 4 residues, 1 model selected
> select #13/S:70
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #13/S:70
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #13/S:69-70
30 atoms, 29 bonds, 2 residues, 1 model selected
> select #13/S:68-70
41 atoms, 40 bonds, 3 residues, 1 model selected
> select #13/S:97
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #13/S:97-101
72 atoms, 71 bonds, 5 residues, 1 model selected
> ui mousemode right select
> select clear
> show #!2 models
> hide #!2 models
> ui mousemode right swapaa
> swapaa mousemode #13/S:97 CYS
> ui mousemode right swapaa
> swapaa mousemode #13/S:97 CYS
> swapaa #13/S:97 asn
Using Dunbrack library
bestfit_AP2nef_08122025.pdb #13/S CYS 97: phi 56.7, psi 18.5 trans
Density criteria with multiple volume models open;
Need to specify one to use via 'density' keyword.
> hide #!13 atoms
[Repeated 1 time(s)]
> hide #!13 surfaces
> show #!13 atoms
> swapaa #13/S:97 asn
Using Dunbrack library
bestfit_AP2nef_08122025.pdb #13/S CYS 97: phi 56.7, psi 18.5 trans
Density criteria with multiple volume models open;
Need to specify one to use via 'density' keyword.
> swapaa #13/S:97 asn density #2
Using Dunbrack library
bestfit_AP2nef_08122025.pdb #13/S CYS 97: phi 56.7, psi 18.5 trans
Applying ASN rotamer (chi angles: 63.8 -26.4) to bestfit_AP2nef_08122025.pdb
#13/S ASN 97
> show #!2 models
> ui mousemode right select
> select #13/S:97@CG
1 atom, 1 residue, 1 model selected
> ui mousemode right swapaa
> swapaa #13/S:97
Missing or invalid "resTypes" argument: Expected a text string
> hide sel atoms
[Repeated 1 time(s)]
> show sel cartoons
> select add #13
23386 atoms, 23612 bonds, 1 pseudobond, 1575 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> hide #!2 models
> ui mousemode right select
> select clear
> select #13/S:97
10 atoms, 9 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!2 models
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
Chain information for bestfit_AP2nef_08122025.pdb
---
Chain | Description
13.2/A | No description available
13.2/B | No description available
13.2/M | No description available
13.2/N | No description available
13.2/S | No description available
Drag select of 1 atoms
Drag select of 2 cryosparc_P24_J249_010_volume_map_sharp_resampled.mrc , 1
atoms, 1 residues, 1 bonds
> isolde sim start #13.2/S:97
Sim termination reason: None
ISOLDE: stopped sim
> isolde sim start #13.2/S:97
Sim termination reason: None
ISOLDE: stopped sim
> isolde sim start #13.2/S:97
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> clipper associate #2 toModel #13
Opened cryosparc_P24_J249_010_volume_map_sharp_resampled.mrc as #13.1.1.1,
grid size 97,111,122, pixel 1.24,1.24,1.24, shown at step 1, values float32
> isolde sim start #13.2/S:94-100
ISOLDE: started sim
> isolde sim pause
3 models selected
[Repeated 3 time(s)]
> ui mousemode right select
> select clear
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Volume Viewer"
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/bestfit_AP2nef_110325.pdb
> models #13
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/comparison_processing_2024_2025.cxs
> includeMaps true
——— End of log from Mon Nov 3 11:46:56 2025 ———
opened ChimeraX session
> close #13
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/bestfit_AP2nef_110325.pdb
Chain information for bestfit_AP2nef_110325.pdb #2
---
Chain | Description
A | No description available
B | No description available
M | No description available
N | No description available
S | No description available
> hide #!2 atoms
> show #!2 cartoons
> show #!12 models
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/cryosparc_P27_J169_006_volume_map_sharp.mrc
Opened cryosparc_P27_J169_006_volume_map_sharp.mrc as #13, grid size
256,256,256, pixel 1.33, shown at level 0.159, step 1, values float32
> hide #!13 models
> show #!13 models
> close #13
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/comparison_processing_2024_2025.cxs
> includeMaps true
——— End of log from Mon Nov 3 11:59:03 2025 ———
opened ChimeraX session
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/cryosparc_P24_J249_010_volume_map_sharp_resampled.mrc
Opened cryosparc_P24_J249_010_volume_map_sharp_resampled.mrc as #13, grid size
97,111,122, pixel 1.24,1.24,1.24, shown at level 2.47, step 1, values float32
> color #13 #b2b2b28a models
> volume #13 level 0.679
> surface dust #13 size 12.4
> volume #13 level 1.192
> volume #13 level 1.278
> volume #13 level 0.8786
> hide #!13 models
> select #2/A
8924 atoms, 9002 bonds, 612 residues, 1 model selected
> color sel cyan
> select #2/B
8188 atoms, 8254 bonds, 564 residues, 1 model selected
> ui tool show "Color Actions"
> color sel chartreuse
> color sel lime
> color sel chartreuse
> select #2/M
1839 atoms, 1860 bonds, 124 residues, 1 model selected
> color sel magenta
> select #2/S
2221 atoms, 2245 bonds, 140 residues, 1 model selected
> ui tool show "Color Actions"
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!14 models
> hide #!14 models
> show #!14 models
> show #!6 models
> hide #!14 models
> hide #!6 models
> ui tool show "Color Actions"
> color sel light coral
> select #2/N
2218 atoms, 2255 bonds, 1 pseudobond, 135 residues, 2 models selected
> color (#!2 & sel) yellow
> ui mousemode right select
> select clear
> show #!13 models
> select add #2
23390 atoms, 23616 bonds, 1 pseudobond, 1575 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> hide sel cartoons
> show sel atoms
> hide sel atoms
> hide sel surfaces
> show sel surfaces
> select #2/S:97
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel surfaces
> show sel atoms
> style sel sphere
Changed 14 atom styles
> style sel stick
Changed 14 atom styles
> color (#!2 & sel) byelement
> select #2/S:99
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel surfaces
> show sel atoms
> style sel ball
Changed 11 atom styles
> color (#!2 & sel) byelement
> select clear
> select #2/S:99
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel ball
Changed 11 atom styles
> style sel sphere
Changed 11 atom styles
> style sel ball
Changed 11 atom styles
> select clear
> volume #13 level 0.8786
> select #2/S:97
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel surfaces
[Repeated 1 time(s)]
> ui tool show "Color Actions"
> color sel light coral
> select clear
Drag select of bestfit_AP2nef_110325.pdb_N SES surface, 221 of 211812
triangles, bestfit_AP2nef_110325.pdb_S SES surface, 136 of 192552 triangles,
13 cryosparc_P24_J249_010_volume_map_sharp_resampled.mrc
> select clear
> hide #!13 models
> hide #!2 surfaces
> show #!2 cartoons
> select #2/N:166
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 14 atom styles
> show #!13 models
> hide #!13 models
> select #2/N:165
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 14 atom styles
> show #!13 models
> show sel surfaces
[Repeated 1 time(s)]
> select #13
2 models selected
> show #!2 surfaces
> select clear
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/cs_p24_j249_resampled_sharp_with_modelvolume.png
> width 1749 height 1129 supersample 2 transparentBackground true
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/cs_p24_j249_resampled_sharp_with_modelvolume_zoom.png
> width 1749 height 1129 supersample 2 transparentBackground true
> select #2/S:99
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel surfaces
> ui tool show "Color Actions"
> color sel light coral
> color (#!2 & sel) byhetero
> select clear
> hide #!13 models
> show #!13 models
> hide #!13 models
> select #2/S:105
20 atoms, 20 bonds, 1 residue, 1 model selected
> hide sel surfaces
> show sel atoms
> style sel ball
Changed 20 atom styles
> color (#!2 & sel) byhetero
> show #!13 models
> hide #!13 models
> select #2/S:102
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel surfaces
> style sel ball
Changed 12 atom styles
> style sel ball
Changed 12 atom styles
> show sel atoms
> color (#!2 & sel) byhetero
> show #!13 models
> select clear
> select #2/N:165
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel surfaces
> show sel atoms
> style sel ball
Changed 14 atom styles
> color (#!2 & sel) byhetero
> select clear
> hide #!13 models
> select #2/S:101
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel surfaces
> show sel atoms
> style sel ball
Changed 19 atom styles
> color (#!2 & sel) byhetero
> select clear
> show #!13 models
> select #2/S:101
19 atoms, 18 bonds, 1 residue, 1 model selected
> color (#!2 & sel) byelement
> hide #!13 models
> select #2/S:105,102,99
43 atoms, 41 bonds, 3 residues, 1 model selected
> color (#!2 & sel) byelement
> select #2/N:165
14 atoms, 13 bonds, 1 residue, 1 model selected
> color (#!2 & sel) byelement
> select clear
> show #!13 models
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/cs_p24_j249_resampled_sharp_with_modelvolume_zoom_topview_contacts.png
> width 1749 height 1129 supersample 1 transparentBackground true
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/cs_p24_j249_resampled_sharp_with_modelvolume_zoom_topview_contacts_v2.png
> width 1749 height 1129 supersample 1 transparentBackground true
> hide #!13 models
> show #!13 models
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/cs_p24_j249_resampled_sharp_with_modelvolume_zoom_topview_contacts_profile.png
> width 1749 height 1129 supersample 1 transparentBackground true
> hide #!2 models
> hide #!13 models
> show #1 models
> show #1 cartoons
> show #!13 models
> hide #1 models
> show #1 models
> hide #1 models
> show #!2 models
> select clear
[Repeated 2 time(s)]
> cofr frontCenter
> select clear
> show #11 models
> hide #!13 models
> hide #!2 models
Drag select of 2 residues
> select clear
> select #11:344-392
387 atoms, 396 bonds, 49 residues, 1 model selected
> color sel cyan
> select clear
> select #11:346
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 11 atom styles
> select clear
> select #11:352
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 8 atom styles
> select #11:366-368
24 atoms, 23 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 24 atom styles
> select clear
> show #!6 models
> hide #!6 models
> show #!13 models
> show #!2 models
> show #!3 models
> volume #3 level 0.2407
> select add #11
3748 atoms, 3849 bonds, 480 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.64807,-0.11079,-0.75348,195.91,-0.74646,-0.28857,-0.5996,208.77,-0.151,0.95103,-0.26972,250.6
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.88247,0.092663,0.46115,200.04,0.44567,0.14875,-0.88275,204.59,-0.15039,0.98452,0.089968,252
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.88247,0.092663,0.46115,188.55,0.44567,0.14875,-0.88275,201.57,-0.15039,0.98452,0.089968,252.87
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.24826,-0.41178,0.87682,193.27,0.83341,0.37057,0.41,205.69,-0.49375,0.83254,0.25118,254.45
> view matrix models
> #11,-0.3734,-0.13114,0.91835,193.19,0.72243,0.57991,0.37656,205.4,-0.58195,0.80406,-0.1218,253.15
> view matrix models
> #11,-0.5057,-0.22411,0.83309,193.25,0.53559,0.67548,0.50682,206.12,-0.67632,0.7025,-0.22156,253.1
> hide #!3 models
> view matrix models
> #11,-0.73922,-0.59528,0.31495,192.24,-0.09467,0.55486,0.82654,208.83,-0.66677,0.58118,-0.46652,252.3
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.73922,-0.59528,0.31495,191.69,-0.09467,0.55486,0.82654,209.03,-0.66677,0.58118,-0.46652,254.78
> view matrix models
> #11,-0.73922,-0.59528,0.31495,191,-0.09467,0.55486,0.82654,208.89,-0.66677,0.58118,-0.46652,253.84
> view matrix models
> #11,-0.73922,-0.59528,0.31495,191.52,-0.09467,0.55486,0.82654,208.96,-0.66677,0.58118,-0.46652,253.55
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.88862,-0.41984,0.18465,190.97,-0.10918,0.58466,0.8039,208.85,-0.44547,0.6942,-0.56538,252.53
> view matrix models
> #11,-0.85479,-0.46923,0.22172,191.14,-0.10632,0.57649,0.81015,208.88,-0.50797,0.66894,-0.54267,252.79
> view matrix models
> #11,-0.90186,-0.39796,0.16815,190.89,-0.11019,0.58823,0.80115,208.83,-0.41773,0.704,-0.57435,252.43
> view matrix models
> #11,0.51397,0.49705,0.69913,188.79,0.82537,-0.064561,-0.56088,202.67,-0.23365,0.86532,-0.44343,252.33
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.51397,0.49705,0.69913,203.91,0.82537,-0.064561,-0.56088,201.71,-0.23365,0.86532,-0.44343,259.39
> view matrix models
> #11,0.51397,0.49705,0.69913,203.27,0.82537,-0.064561,-0.56088,202.78,-0.23365,0.86532,-0.44343,252.8
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.52663,0.49904,0.6882,203.2,0.81648,-0.071517,-0.57293,202.76,-0.2367,0.86362,-0.44512,252.8
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.52663,0.49904,0.6882,202.05,0.81648,-0.071517,-0.57293,201.74,-0.2367,0.86362,-0.44512,252.18
> view matrix models
> #11,0.52663,0.49904,0.6882,206.71,0.81648,-0.071517,-0.57293,199.76,-0.2367,0.86362,-0.44512,250.25
> view matrix models
> #11,0.52663,0.49904,0.6882,206.58,0.81648,-0.071517,-0.57293,198.09,-0.2367,0.86362,-0.44512,255.9
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.27402,0.45257,0.84858,207.79,0.91259,0.15607,-0.37792,198.3,-0.30347,0.87797,-0.37024,256.3
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.27402,0.45257,0.84858,206.4,0.91259,0.15607,-0.37792,197.74,-0.30347,0.87797,-0.37024,253.54
> ui mousemode right select
> select clear
> select add #11
3748 atoms, 3849 bonds, 480 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.27402,0.45257,0.84858,204.56,0.91259,0.15607,-0.37792,198.64,-0.30347,0.87797,-0.37024,251.99
> select subtract #11
Nothing selected
> ui mousemode right "rotate selected models"
> select add #13
3 models selected
> view matrix models
> #13,0.99385,0.080221,0.076372,-27.987,-0.08412,0.99524,0.049272,9.0037,-0.072056,-0.055393,0.99586,25.956
> select subtract #13
Nothing selected
> undo
[Repeated 1 time(s)]
> select subtract #13
Nothing selected
> select add #11
3748 atoms, 3849 bonds, 480 residues, 1 model selected
> view matrix models
> #11,0.34539,0.61257,0.71096,203.58,0.92387,-0.088877,-0.37224,199.07,-0.16484,0.7854,-0.59664,250.97
> view matrix models
> #11,0.33564,0.58556,0.73788,203.76,0.91281,-0.008711,-0.40829,198.8,-0.23265,0.81058,-0.53743,251.3
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.33564,0.58556,0.73788,210.32,0.91281,-0.008711,-0.40829,192.61,-0.23265,0.81058,-0.53743,250.57
> view matrix models
> #11,0.33564,0.58556,0.73788,208.48,0.91281,-0.008711,-0.40829,187.9,-0.23265,0.81058,-0.53743,251.35
> view matrix models
> #11,0.33564,0.58556,0.73788,210.01,0.91281,-0.008711,-0.40829,187.91,-0.23265,0.81058,-0.53743,251.05
> select add #12
27061 atoms, 27388 bonds, 1 pseudobond, 2055 residues, 3 models selected
> select subtract #11
23313 atoms, 23539 bonds, 1 pseudobond, 1575 residues, 2 models selected
> select subtract #12
Nothing selected
> select add #11
3748 atoms, 3849 bonds, 480 residues, 1 model selected
> view matrix models
> #11,0.33564,0.58556,0.73788,210.72,0.91281,-0.008711,-0.40829,186.69,-0.23265,0.81058,-0.53743,253.36
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.42674,0.6292,0.64962,210.11,0.84806,-0.028892,-0.52911,186.35,-0.31415,0.77671,-0.54593,253.54
> view matrix models
> #11,0.43774,0.61225,0.65843,210.16,0.85392,-0.053884,-0.51761,186.43,-0.28143,0.78882,-0.5464,253.45
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.43774,0.61225,0.65843,210.26,0.85392,-0.053884,-0.51761,187.42,-0.28143,0.78882,-0.5464,253.55
> show #!3 models
> volume #3 level 0.08929
> select subtract #11
Nothing selected
> volume #3 level 0.1329
> hide #11 models
> show #11 models
> select add #11
3748 atoms, 3849 bonds, 480 residues, 1 model selected
> view matrix models
> #11,0.43774,0.61225,0.65843,209.39,0.85392,-0.053884,-0.51761,189.92,-0.28143,0.78882,-0.5464,254
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.21435,-0.44068,-0.8717,206.26,-0.91836,-0.21304,0.33352,197.02,-0.33268,0.87202,-0.35903,254.71
> view matrix models
> #11,-0.17968,-0.53738,-0.82398,206.56,-0.9824,0.054639,0.1786,196.04,-0.050954,0.84157,-0.53774,253.5
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.17968,-0.53738,-0.82398,201.93,-0.9824,0.054639,0.1786,209.1,-0.050954,0.84157,-0.53774,254.05
> view matrix models
> #11,-0.17968,-0.53738,-0.82398,197.13,-0.9824,0.054639,0.1786,210.39,-0.050954,0.84157,-0.53774,256.02
> hide #!3 models
> view matrix models
> #11,-0.17968,-0.53738,-0.82398,197.61,-0.9824,0.054639,0.1786,210.72,-0.050954,0.84157,-0.53774,255.89
> show #!3 models
> volume #3 level 0.1201
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.88371,-0.31387,0.34719,203.31,-0.15221,0.89422,0.42096,208.65,-0.44259,0.31916,-0.838,256.33
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.88371,-0.31387,0.34719,194.08,-0.15221,0.89422,0.42096,210.95,-0.44259,0.31916,-0.838,250.91
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.96557,-0.24904,0.075168,193.01,-0.196,0.88647,0.41923,211.04,-0.17104,0.39007,-0.90476,249.99
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.96557,-0.24904,0.075168,193.47,-0.196,0.88647,0.41923,212.64,-0.17104,0.39007,-0.90476,250.56
> volume #3 level 0.1201
> hide #!3 models
> view matrix models
> #11,-0.96557,-0.24904,0.075168,194.01,-0.196,0.88647,0.41923,216.6,-0.17104,0.39007,-0.90476,251.58
> view matrix models
> #11,-0.96557,-0.24904,0.075168,203.91,-0.196,0.88647,0.41923,218.46,-0.17104,0.39007,-0.90476,247.81
> view matrix models
> #11,-0.96557,-0.24904,0.075168,205.22,-0.196,0.88647,0.41923,218.39,-0.17104,0.39007,-0.90476,248.54
> show #!3 models
> hide #!3 models
> select subtract #11
Nothing selected
> hide #!13 models
> hide #!2 models
> select #11:346,352,366-368
43 atoms, 40 bonds, 5 residues, 1 model selected
> color sel byelement
> ui mousemode right select
> select clear
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/Serinc5_contacts_dock_run3_matches_density.png
> width 1749 height 1129 supersample 1 transparentBackground true
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/comparison_processing_2024_2025_withdocking_residues.cxs
> includeMaps true
——— End of log from Mon Nov 3 13:41:56 2025 ———
opened ChimeraX session
> ui tool show "Side View"
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/Serinc_dock_res_zoom.png
> width 1749 height 1129 supersample 1 transparentBackground true
> ui mousemode right select
> select #11/A:357
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #11/A:360
12 atoms, 10 bonds, 2 residues, 1 model selected
> select add #11/A:358
18 atoms, 15 bonds, 3 residues, 1 model selected
> style sel ball
Changed 18 atom styles
> show sel atoms
> color sel byelement
> select clear
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/Serinc_dock_res_zoom_withCys.png
> width 1749 height 1129 supersample 1 transparentBackground true
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/comparison_processing_2024_2025_withdocking_residues.cxs
Opened denmod_map_sharpened.ccp4 as #4, grid size 97,111,122, pixel 1.24,
shown at level 1.37, step 1, values float32
Opened cryosparc_P24_J221_volume_map_consensus.mrc as #5, grid size
144,144,144, pixel 2.86, shown at level 0.696, step 1, values float32
Opened cryosparc_P27_J86_004_volume_map.mrc as #3, grid size 256,256,256,
pixel 1.33, shown at level 0.12, step 1, values float32
Opened cryosparc_P27_J169_006_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 1.33, shown at level 0.624, step 1, values float32
Opened denmod_map_sharpened.ccp4 as #8, grid size 256,256,256, pixel 1.33,
shown at level 0.115, step 1, values float32
Opened cryosparc_P27_J141_flex_map.mrc as #10, grid size 256,256,256, pixel
1.33, shown at level 0.00547, step 1, values float32
Opened cryosparc_P24_J249_010_volume_map_sharp_resampled.mrc as #13, grid size
97,111,122, pixel 1.24,1.24,1.24, shown at level 0.879, step 1, values float32
Log from Mon Nov 3 13:41:56 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/comparison_processing_2024_2025.cxs
Opened denmod_map_sharpened.ccp4 as #4, grid size 97,111,122, pixel 1.24,
shown at level 1.37, step 1, values float32
Opened cryosparc_P24_J221_volume_map_consensus.mrc as #5, grid size
144,144,144, pixel 2.86, shown at level 0.696, step 1, values float32
Opened cryosparc_P27_J86_004_volume_map.mrc as #3, grid size 256,256,256,
pixel 1.33, shown at level 0.102, step 1, values float32
Opened cryosparc_P27_J169_006_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 1.33, shown at level 0.624, step 1, values float32
Opened denmod_map_sharpened.ccp4 as #8, grid size 256,256,256, pixel 1.33,
shown at level 0.115, step 1, values float32
Opened cryosparc_P27_J141_flex_map.mrc as #10, grid size 256,256,256, pixel
1.33, shown at level 0.00547, step 1, values float32
Log from Mon Nov 3 11:59:03 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/comparison_processing_2024_2025.cxs
Opened denmod_map_sharpened.ccp4 as #4, grid size 97,111,122, pixel 1.24,
shown at level 1.37, step 1, values float32
Opened cryosparc_P24_J221_volume_map_consensus.mrc as #5, grid size
144,144,144, pixel 2.86, shown at level 0.696, step 1, values float32
Opened cryosparc_P27_J86_004_volume_map.mrc as #3, grid size 256,256,256,
pixel 1.33, shown at level 0.102, step 1, values float32
Opened cryosparc_P27_J169_006_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 1.33, shown at level 0.624, step 1, values float32
Opened denmod_map_sharpened.ccp4 as #8, grid size 256,256,256, pixel 1.33,
shown at level 0.115, step 1, values float32
Opened cryosparc_P27_J141_flex_map.mrc as #10, grid size 256,256,256, pixel
1.33, shown at level 0.00547, step 1, values float32
Opened cryosparc_P24_J249_010_volume_map_sharp_resampled.mrc as #13.1.1.1,
grid size 97,111,122, pixel 1.24,1.24,1.24, shown at level 2.07, step 1,
values float32
Log from Mon Nov 3 11:46:56 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/comparison_processing_2024_2025.cxs
Opened cryosparc_P24_J249_010_volume_map_sharp_resampled.mrc as #2, grid size
97,111,122, pixel 1.24,1.24,1.24, shown at level 1.82, step 1, values float32
Opened denmod_map_sharpened.ccp4 as #4, grid size 97,111,122, pixel 1.24,
shown at level 1.37, step 1, values float32
Opened cryosparc_P24_J221_volume_map_consensus.mrc as #5, grid size
144,144,144, pixel 2.86, shown at level 0.845, step 1, values float32
Opened cryosparc_P27_J86_004_volume_map.mrc as #3, grid size 256,256,256,
pixel 1.33, shown at level 0.11, step 1, values float32
Opened cryosparc_P27_J169_006_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 1.33, shown at level 0.516, step 1, values float32
Opened denmod_map_sharpened.ccp4 as #8, grid size 256,256,256, pixel 1.33,
shown at level 0.115, step 1, values float32
Opened cryosparc_P27_J141_flex_map.mrc as #10, grid size 256,256,256, pixel
1.33, shown at level 0.00547, step 1, values float32
Log from Thu Sep 18 21:45:21 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/comparison_processing_2024_2025.cxs
Opened cryosparc_P24_J249_010_volume_map_sharp_resampled.mrc as #2, grid size
97,111,122, pixel 1.24,1.24,1.24, shown at level 0.733, step 1, values float32
Opened denmod_map_sharpened.ccp4 as #4, grid size 97,111,122, pixel 1.24,
shown at level 0.373, step 1, values float32
Opened cryosparc_P24_J221_volume_map_consensus.mrc as #5, grid size
144,144,144, pixel 2.86, shown at level 0.758, step 1, values float32
Opened cryosparc_P27_J86_004_volume_map.mrc as #3, grid size 256,256,256,
pixel 1.33, shown at level 0.11, step 1, values float32
Opened cryosparc_P27_J169_006_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 1.33, shown at level 0.287, step 1, values float32
Opened denmod_map_sharpened.ccp4 as #8, grid size 256,256,256, pixel 1.33,
shown at level 0.062, step 1, values float32
Opened cryosparc_P27_J141_flex_map.mrc as #10, grid size 256,256,256, pixel
1.33, shown at level 0.00547, step 1, values float32
Log from Mon Aug 18 17:27:18 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/Serinc5Ap2Nef_project_maps_withdocking_04172025.cxs
Opened cryosparc_P24_J249_010_volume_map_sharp_resampled.mrc as #2, grid size
97,111,122, pixel 1.24,1.24,1.24, shown at level 1.31, step 1, values float32
Opened denmod_map_sharpened.ccp4 as #4, grid size 97,111,122, pixel 1.24,
shown at level 1.74, step 1, values float32
Opened cryosparc_P24_J249_010_volume_map_resampled.mrc as #3, grid size
97,111,122, pixel 1.24,1.24,1.24, shown at level 0.762, step 1, values float32
Opened cryosparc_P24_J221_volume_map_consensus.mrc as #5, grid size
144,144,144, pixel 2.86, shown at level 0.758, step 1, values float32
Log from Thu Apr 17 14:19:45 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/Serinc5Ap2Nef_project_maps_models_03032025.cxs
Opened cryosparc_P24_J249_010_volume_map_sharp_resampled.mrc as #2, grid size
97,111,122, pixel 1.24,1.24,1.24, shown at level 1.23, step 1, values float32
Opened denmod_map_sharpened.ccp4 as #4, grid size 97,111,122, pixel 1.24,
shown at level 0.644, step 1, values float32
Opened cryosparc_P24_J249_010_volume_map_resampled.mrc as #3, grid size
97,111,122, pixel 1.24,1.24,1.24, shown at level 0.916, step 1, values float32
Opened cryosparc_P24_J221_volume_map_consensus.mrc as #5, grid size
144,144,144, pixel 2.86, shown at level 1.73, step 1, values float32
Log from Sun Mar 2 22:52:36 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/Serinc5Ap2Nef_project_maps_models_02252025.cxs
Opened cryosparc_P24_J249_010_volume_map_sharp_resampled.mrc as #2, grid size
97,111,122, pixel 1.24,1.24,1.24, shown at level 1.23, step 1, values float32
Opened denmod_map_sharpened.ccp4 as #4, grid size 97,111,122, pixel 1.24,
shown at level 0.644, step 1, values float32
Opened cryosparc_P24_J249_010_volume_map_resampled.mrc as #3, grid size
97,111,122, pixel 1.24,1.24,1.24, shown at level 0.916, step 1, values float32
Opened cryosparc_P24_J221_volume_map_consensus.mrc as #5, grid size
144,144,144, pixel 2.86, shown at level 1.73, step 1, values float32
Log from Tue Feb 25 18:08:00 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/Serinc5Ap2Nef_project_02112025.cxs
Opened cryosparc_P24_J249_010_volume_map_sharp_resampled.mrc as #2, grid size
97,111,122, pixel 1.24,1.24,1.24, shown at level 1.23, step 1, values float32
Opened denmod_map_sharpened.ccp4 as #4, grid size 97,111,122, pixel 1.24,
shown at level 1.29, step 1, values float32
Opened cryosparc_P24_J249_010_volume_map_resampled.mrc as #3, grid size
97,111,122, pixel 1.24,1.24,1.24, shown at level 0.587, step 1, values float32
Log from Tue Feb 11 16:42:50 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/bestfit_AP2Nef_021125.pdb
Chain information for bestfit_AP2Nef_021125.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
M | No description available
S | No description available
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/cryosparc_P24_J249_010_volume_map_sharp_resampled.mrc
Opened cryosparc_P24_J249_010_volume_map_sharp_resampled.mrc as #2, grid size
97,111,122, pixel 1.24,1.24,1.24, shown at level 2.47, step 1, values float32
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/cryosparc_P24_J250_volume_map_sharp_resampled.mrc
Opened cryosparc_P24_J250_volume_map_sharp_resampled.mrc as #3, grid size
97,111,122, pixel 1.24,1.24,1.24, shown at level 1.72, step 1, values float32
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/Phenixjobs/LocalAnisoSharpen_41/denmod_map_sharpened.ccp4
Opened denmod_map_sharpened.ccp4 as #4, grid size 97,111,122, pixel 1.24,
shown at level 3.91, step 1, values float32
> set bgColor white
> hide atoms
> show cartoons
> select add #1
23300 atoms, 23525 bonds, 1575 residues, 1 model selected
> ui tool show "Color Actions"
> color sel bychain
> select subtract #1
Nothing selected
> graphics silhouettes true
> lighting full
> volume #2 level 1.229
> close #3
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/cryosparc_P24_J249_010_volume_map_resampled.mrc
Opened cryosparc_P24_J249_010_volume_map_resampled.mrc as #3, grid size
97,111,122, pixel 1.24,1.24,1.24, shown at level 1.48, step 1, values float32
> volume #3 level 0.5866
> volume #3 color #b2b2ff7a
> volume #4 level 1.779
> surface dust #2 size 12.4
> surface dust #4 size 12.4
> surface dust #3 size 12.4
> volume #4 level 1.197
> volume #4 level 1.536
> volume #4 level 1.294
Cell requested for row 0 is out of bounds for table with 0 rows! Resizing
table model.
[Repeated 1 time(s)]
> select /C:81-210
2123 atoms, 2161 bonds, 130 residues, 1 model selected
Cell requested for row 0 is out of bounds for table with 0 rows! Resizing
table model.
> sequence chain #1/C
Alignment identifier is 1/C
Cell requested for row 0 is out of bounds for table with 0 rows! Resizing
table model.
[Repeated 1 time(s)]
> sequence chain #1/D
Alignment identifier is 1/D
Cell requested for row 0 is out of bounds for table with 0 rows! Resizing
table model.
> sequence chain #1/D
Destroying pre-existing alignment with identifier 1/D
Alignment identifier is 1/D
Cell requested for row 0 is out of bounds for table with 0 rows! Resizing
table model.
> select /D:1-2
31 atoms, 30 bonds, 2 residues, 1 model selected
> select /D
95 atoms, 94 bonds, 5 residues, 1 model selected
> ui tool show "Renumber Residues"
> renumber /D seqStart 15
5 residues renumbered
> renumber /C seqStart 109
130 residues renumbered
> ui tool show "Renumber Residues"
> help help:user/tools/renumber.html
> ui tool show "Change Chain IDs"
> changechains sel C,D N,N
Chain IDs of 5 residues changed
> changechains sel C N
No residues specified have any of the 'from' chain IDs
> ui tool show "Change Chain IDs"
> select /N:15-16
31 atoms, 30 bonds, 2 residues, 1 model selected
> select /N
95 atoms, 94 bonds, 5 residues, 1 model selected
> select /C:109-110
38 atoms, 38 bonds, 2 residues, 1 model selected
> select /C
2123 atoms, 2161 bonds, 130 residues, 1 model selected
> ui mousemode right select
> hide #!3 models
Drag select of 5 residues
> changechains sel N
Chain IDs of 130 residues changed
> select add #1
23300 atoms, 23525 bonds, 1575 residues, 1 model selected
Alignment identifier is 1/B
Alignment identifier is 1/A
Alignment identifier is 1/S
Alignment identifier is 1/M
Chains must have same sequence
> select #1/N
2218 atoms, 2255 bonds, 135 residues, 1 model selected
Chains must have same sequence
> close #1
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/bestfit_AP2Nef_021125.pdb
Chain information for bestfit_AP2Nef_021125.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
M | No description available
S | No description available
> hide atoms
> show cartoons
> show #!3 models
> hide #!2 models
> hide #!4 models
> show #!4 models
Drag select of 4 denmod_map_sharpened.ccp4 , 3
cryosparc_P24_J249_010_volume_map_resampled.mrc , 12 residues
> select clear
[Repeated 1 time(s)]
> ui mousemode right translate
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/side_view_extradensity.png
> width 1821 height 1179 supersample 2 transparentBackground true
> hide #!3 models
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/Serinc5Ap2Nef_project_02112025.cxs
> includeMaps true
——— End of log from Tue Feb 11 16:42:50 2025 ———
opened ChimeraX session
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> color #4 #b2ffff7f models
> color #4 #b2ffff80 models
> select add #1
23300 atoms, 23525 bonds, 1575 residues, 1 model selected
> ui tool show "Color Actions"
> color sel bychain
> hide #!4 models
> show #!4 models
> select subtract #1
Nothing selected
> volume #4 level 0.9439
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/joanapaulino/Desktop/movie38.mp4
Movie saved to /Users/joanapaulino/Desktop/movie38.mp4
> select clear
> select /D:5
25 atoms, 24 bonds, 1 residue, 1 model selected
> select ~sel
23275 atoms, 23500 bonds, 1574 residues, 7 models selected
> select down
23275 atoms, 23500 bonds, 1574 residues, 7 models selected
> select clear
> hide #!4 models
Drag select of 1 residues
Drag select of 5 residues
> show sel cartoons
> hide sel cartoons
> show #!4 models
> color #4 #b2ffff5f models
> color #4 #b2ffff5a models
> color #4 #d2fff55a models
> color #4 #d2fff559 models
> lighting shadows false
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/joanapaulino/Desktop/movie39.mp4
Movie saved to /Users/joanapaulino/Desktop/movie39.mp4
> select add #1
23300 atoms, 23525 bonds, 1575 residues, 1 model selected
> show sel surfaces
[Repeated 1 time(s)]
> select /D:5@NE
1 atom, 1 residue, 1 model selected
> select ~sel
23299 atoms, 23522 bonds, 1575 residues, 7 models selected
> select ~sel
1 atom, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 2 models selected
> select /D:1@HA
1 atom, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 2 models selected
> select /D:5@NH1
1 atom, 1 residue, 1 model selected
> select ~sel
23299 atoms, 23522 bonds, 1575 residues, 7 models selected
> select ~sel
1 atom, 1 residue, 1 model selected
> select ~sel
23299 atoms, 23522 bonds, 1575 residues, 7 models selected
> select ~sel
1 atom, 1 residue, 1 model selected
> hide #!4 models
> select /D:3@NH1
1 atom, 1 residue, 1 model selected
> select up
24 atoms, 23 bonds, 1 residue, 2 models selected
> select up
95 atoms, 94 bonds, 5 residues, 2 models selected
> hide sel surfaces
> show #!4 models
> volume #4 level 0.6441
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/joanapaulino/Desktop/movie38.mp4
Movie saved to /Users/joanapaulino/Desktop/movie38.mp4
> show #!3 models
> hide #!4 models
> hide #!1 models
> volume #3 level 0.4184
> volume #3 level 0.5427
> show #!1 models
> volume #3 level 0.5939
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/joanapaulino/Desktop/movie38.mp4
Movie saved to /Users/joanapaulino/Desktop/movie38.mp4
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/cryosparc_P24_J221_volume_map_consensus.mrc
Opened cryosparc_P24_J221_volume_map_consensus.mrc as #5, grid size
144,144,144, pixel 2.86, shown at level 0.46, step 1, values float32
> ui tool show "Fit in Map"
> fitmap #5 inMap #2
Fit map cryosparc_P24_J221_volume_map_consensus.mrc in map
cryosparc_P24_J249_010_volume_map_sharp_resampled.mrc using 29853 points
correlation = 0.6993, correlation about mean = 0.5935, overlap = 2.418e+04
steps = 208, shift = 9.97, angle = 0.591 degrees
Position of cryosparc_P24_J221_volume_map_consensus.mrc (#5) relative to
cryosparc_P24_J249_010_volume_map_sharp_resampled.mrc (#2) coordinates:
Matrix rotation and translation
0.99994840 -0.00953936 0.00349179 -5.14621176
0.00953299 0.99995287 0.00183650 -7.91370651
-0.00350914 -0.00180312 0.99999222 -4.11791779
Axis -0.17633736 0.33919048 0.92404272
Axis point 628.33698722 -646.05332744 0.00000000
Rotation angle (degrees) 0.59130603
Shift along axis -5.58191648
> volume #5 level 0.7708
> volume #5 level 1.069
> hide #!3 models
> color #5 #ffb2ff86 models
> color #5 #ffb2ff85 models
> volume #5 level 0.9201
> volume #5 level 1.442
> show #!3 models
> hide #!3 models
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/Serinc5Ap2Nef_project_02252025.cxs
> includeMaps true
> hide #!5 models
> show sel cartoons
> hide sel surfaces
[Repeated 4 time(s)]
> select clear
> hide surfaces
> open "/Users/joanapaulino/Documents/postdoc_UCSF/Serinc/Nef_AP2
> structures/Nef_AP2_noTet.pdb"
Chain information for Nef_AP2_noTet.pdb #6
---
Chain | Description
A | No description available
B | No description available
M | No description available
N | No description available
S | No description available
> hide atoms
> show cartoons
> ui tool show Matchmaker
> matchmaker #!6 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker bestfit_AP2Nef_021125.pdb, chain A (#1) with Nef_AP2_noTet.pdb,
chain A (#6), sequence alignment score = 2903.7
RMSD between 217 pruned atom pairs is 0.912 angstroms; (across all 590 pairs:
5.521)
> matchmaker #!6 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker bestfit_AP2Nef_021125.pdb, chain A (#1) with Nef_AP2_noTet.pdb,
chain A (#6), sequence alignment score = 2903.7
RMSD between 217 pruned atom pairs is 0.912 angstroms; (across all 590 pairs:
5.521)
> select add #6
11575 atoms, 11796 bonds, 1 pseudobond, 1565 residues, 2 models selected
> color (#!6 & sel) dark gray
> select clear
> open "/Users/joanapaulino/Documents/postdoc_UCSF/Serinc/Nef_AP2
> structures/6owt.pdb"
6owt.pdb title:
Structure of sivsmm nef and SMM tetherin bound to the clathrin adaptor ap-2
complex [more info...]
Chain information for 6owt.pdb #7
---
Chain | Description | UniProt
A | ap-2 complex subunit α | Q66HM2_RAT 1-939
B | ap-2 complex subunit β | AP2B1_RAT 1-591
M | adaptor protein complex ap-2, Μ1 | Q5FWI9_MOUSE 1-141
N T | tetherin,protein nef | C3VHQ5_CERAT -32--12 -4-16, Q4JGV0_SIV 1-251 29-270
S | ap-2 complex subunit σ | AP2S1_RAT 1-142
> hide atoms
> show cartoons
> color #1,6-7 dark gray
> select add #1
23300 atoms, 23525 bonds, 1575 residues, 1 model selected
> ui tool show "Color Actions"
> color sel bychain
> select subtract #1
6 models selected
> ui tool show Matchmaker
> matchmaker #!7 to #6
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 Nef_AP2_noTet.pdb, chain A (#6) with 6owt.pdb, chain A (#7),
sequence alignment score = 3048
RMSD between 590 pruned atom pairs is 0.000 angstroms; (across all 590 pairs:
0.000)
> matchmaker #!7 to #6
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 Nef_AP2_noTet.pdb, chain A (#6) with 6owt.pdb, chain A (#7),
sequence alignment score = 3048
RMSD between 590 pruned atom pairs is 0.000 angstroms; (across all 590 pairs:
0.000)
> hide #!6 models
Cell requested for row 0 is out of bounds for table with 0 rows! Resizing
table model.
> select #7/T:3-12
74 atoms, 76 bonds, 10 residues, 1 model selected
Cell requested for row 0 is out of bounds for table with 0 rows! Resizing
table model.
> select #7/T:3-12
74 atoms, 76 bonds, 10 residues, 1 model selected
> color sel red
> select clear
> hide #!1 models
> show #!3 models
> show #!5 models
> hide #!3 models
> volume #5 level 1.355
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> show #!3 models
> show #!7 models
> hide #!6 models
> hide #!5 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!4 models
> hide #!3 models
> hide #!4 models
> hide #!7 models
> show #!1 models
> select #1A
Expected an objects specifier or a keyword
> select #1/a
8890 atoms, 8968 bonds, 612 residues, 1 model selected
> select #1/A:11,43,57,58,61
111 atoms, 108 bonds, 5 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 111 atom styles
> select clear
> select #1/A:11,43,57,58,61
111 atoms, 108 bonds, 5 residues, 1 model selected
> color (#!1 & sel) byhetero
> select clear
> show #!4 models
> hide #!4 models
> show #!5 models
> volume #5 level 0.8703
> volume #5 level 0.7957
> volume #5 level 0.7708
> volume #5 level 0.9076
> volume #5 level 1.343
> volume #5 level 1.728
> show #!3 models
> hide #!5 models
> volume #3 level 0.9156
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/Serinc5Ap2Nef_project_02252025.cxs
> includeMaps true
——— End of log from Tue Feb 25 18:08:00 2025 ———
opened ChimeraX session
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/bestfit_AP2Nef_030225_Nef.pdb
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/bestfit_AP2Nef_030225_chainS.pdb
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/bestfit_AP2Nef_030225_chainM.pdb
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/bestfit_AP2Nef_030225_chainD.pdb
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/bestfit_AP2Nef_030225_chainC.pdb
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/bestfit_AP2Nef_030225_chainB.pdb
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/bestfit_AP2Nef_030225_chainA.pdb
Summary of feedback from opening
/Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/bestfit_AP2Nef_030225_Nef.pdb
---
warnings | Ignored bad PDB record found on line 115
PDB SEQRES record for chain N is incomplete. Ignoring input sequence records
as basis for sequence.
Chain information for bestfit_AP2Nef_030225_Nef.pdb #8
---
Chain | Description
N | No description available
Chain information for bestfit_AP2Nef_030225_chainS.pdb #9
---
Chain | Description
S | No description available
Chain information for bestfit_AP2Nef_030225_chainM.pdb #10
---
Chain | Description
M | No description available
Chain information for bestfit_AP2Nef_030225_chainD.pdb #11
---
Chain | Description
D | No description available
Chain information for bestfit_AP2Nef_030225_chainC.pdb #12
---
Chain | Description
C | No description available
Chain information for bestfit_AP2Nef_030225_chainB.pdb #13
---
Chain | Description
B | No description available
Chain information for bestfit_AP2Nef_030225_chainA.pdb #14
---
Chain | Description
A | No description available
> hide #!1 models
> hide #9-14#!8 atoms
> close #11
> close #12
> combine #14,#13,#10,#9,#8
Expected a keyword
> combine #14 #13 #10 #9 #8
> hide #!3 models
> show #!3 models
> hide #!8 models
> hide #9 models
> hide #!11 models
> hide #13 models
> hide #14 models
> hide #10 models
> show #!11 models
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/bestfit_AP2Nef_03032025.pdb
> models #11
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/bestfit_AP2Nef_03032025.pdb
Chain information for bestfit_AP2Nef_03032025.pdb #12
---
Chain | Description
A | No description available
B | No description available
M | No description available
N | No description available
S | No description available
> hide #!11-12 atoms
> show #!11-12 cartoons
> close #1
> close #8
> close #9
> close #10
> close #13
> close #14
> hide #!11 models
> hide #!12 models
> show #!11 models
> show #!12 models
> hide #!11 models
> close #11
> select add #12
23313 atoms, 23539 bonds, 1 pseudobond, 1575 residues, 2 models selected
> ui tool show "Color Actions"
> color sel bychain
> select subtract #12
Nothing selected
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/Serinc5Ap2Nef_project_maps_models_03032025.cxs
> includeMaps true
——— End of log from Sun Mar 2 22:52:36 2025 ———
opened ChimeraX session
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/Docking_MD_Serinc5_AP2Nef/cluster2_1.pdb
Summary of feedback from opening
/Users/joanapaulino/Documents/postdoc_UCSF/Serinc/Docking_MD_Serinc5_AP2Nef/cluster2_1.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK FILENAME="complex_119w.pdb0"
Ignored bad PDB record found on line 2
REMARK ===============================================================
Ignored bad PDB record found on line 3
REMARK HADDOCK run for complex
Ignored bad PDB record found on line 4
REMARK initial structure: complex_119.pdb
Ignored bad PDB record found on line 5
REMARK ===============================================================
29 messages similar to the above omitted
Chain information for cluster2_1.pdb #1
---
Chain | Description
A | No description available
B | No description available
> ui tool show Matchmaker
> matchmaker #1 to #12
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 bestfit_AP2Nef_03032025.pdb, chain S (#12) with cluster2_1.pdb,
chain A (#1), sequence alignment score = 720.1
RMSD between 140 pruned atom pairs is 0.530 angstroms; (across all 140 pairs:
0.530)
> hide #!12 models
> select #1/A:1-140
1442 atoms, 1466 bonds, 140 residues, 1 model selected
> select #1/A:1-140
1442 atoms, 1466 bonds, 140 residues, 1 model selected
> select #1/A:1-140
1442 atoms, 1466 bonds, 140 residues, 1 model selected
> color sel red
> volume #3 level 0.3891
> volume #3 level 0.9887
> select #1/A:1-140
1442 atoms, 1466 bonds, 140 residues, 1 model selected
> select #1/A:1-140
1442 atoms, 1466 bonds, 140 residues, 1 model selected
> select #1/A:1-140
1442 atoms, 1466 bonds, 140 residues, 1 model selected
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #1/A
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
> select add #1
5971 atoms, 6096 bonds, 620 residues, 1 model selected
> select subtract #1
Nothing selected
> show #!2 models
> volume #2 level 0.4878
> volume #2 level 1.314
> hide #!2 models
> show #!4 models
> hide #!3 models
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> volume #4 level 2.093
> volume #4 level 1.743
> hide #!4 models
> show #!5 models
> volume #5 level 0.7335
> show #!3 models
> hide #!3 models
> hide #!5 models
> show #!6 models
> show #!5 models
> hide #!6 models
> hide #1 models
> volume #5 level 0.6838
> show #1 models
> show #!12 models
> hide #!5 models
> show #!3 models
> volume #3 level 0.3599
> volume #3 level 0.762
> show #!5 models
> volume #5 level 0.7957
> volume #5 level 0.7584
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/Serinc5Ap2Nef_project_maps_withdocking_04172025.cxs
> includeMaps true
——— End of log from Thu Apr 17 14:19:45 2025 ———
opened ChimeraX session
> hide #1 models
> hide #!5 models
> hide #!3 models
> show #!2 models
> volume #2 level 0.7331
> volume #2 color #7b7b7b
> volume #2 color #b9b9b9
> volume #2 color #b9b9b97b
> color #2 #8279bfff models
> color #2 #5d5fbfff models
> color #2 #7883bfff models
> color #2 #7883bf78 models
> color #2 #cbc5bd78 models
> set bgColor black
> color #2 #c8c9cb78 models
> color #2 #c8c9cb8b models
> show #1 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!2 models
> set bgColor white
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> close #7
> close #3
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/cryosparc_P27_J86_004_volume_map.mrc
Opened cryosparc_P27_J86_004_volume_map.mrc as #3, grid size 256,256,256,
pixel 1.33, shown at level 0.127, step 1, values float32
> ui mousemode right select
> ui mousemode right "translate selected models"
> select add #3
2 models selected
> view matrix models #3,1,0,0,-49.213,0,1,0,-29.446,0,0,1,4.6433
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.49798,-0.828,-0.25776,390.13,-0.86659,0.46408,0.18345,180.28,-0.032273,0.31473,-0.94863,273.72
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.49798,-0.828,-0.25776,471.73,-0.86659,0.46408,0.18345,224,-0.032273,0.31473,-0.94863,295.87
> view matrix models
> #3,-0.49798,-0.828,-0.25776,473.5,-0.86659,0.46408,0.18345,229.8,-0.032273,0.31473,-0.94863,295.04
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.87326,-0.34966,-0.33934,467.95,-0.40204,0.91053,0.096388,88.05,0.27528,0.2206,-0.93571,256.96
> ui tool show "Fit in Map"
> fitmap #3 inMap #4
Fit map cryosparc_P27_J86_004_volume_map.mrc in map denmod_map_sharpened.ccp4
using 167620 points
correlation = 0.3425, correlation about mean = 0.3108, overlap = 3.448e+04
steps = 196, shift = 14, angle = 25 degrees
Position of cryosparc_P27_J86_004_volume_map.mrc (#3) relative to
denmod_map_sharpened.ccp4 (#4) coordinates:
Matrix rotation and translation
-0.96346586 -0.25771906 0.07289920 391.25575931
-0.24462869 0.95759087 0.15223816 51.68881411
-0.10904228 0.12884304 -0.98565162 356.98165676
Axis -0.12721247 0.98931817 0.07117973
Axis point 207.21932702 0.00000000 167.44136265
Rotation angle (degrees) 174.72402992
Shift along axis 26.77392845
> color #3 #bf912aff models
> color #3 #bf912a83 models
> color #3 #bf912a82 models
> color #4 #d2fff5ff models
> ui mousemode right select
> select clear
> color #3 #c0a3cb82 models
> volume #3 level 0.1098
> hide #1 models
> volume #4 level 0.7217
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/cryosparc_P27_J169_006_volume_map_sharp.mrc
Opened cryosparc_P27_J169_006_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 1.33, shown at level 0.159, step 1, values float32
> surface dust #4 size 12.4
> surface dust #3 size 13.3
> surface dust #7 size 13.3
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> fitmap #7 inMap #4
Fit map cryosparc_P27_J169_006_volume_map_sharp.mrc in map
denmod_map_sharpened.ccp4 using 166885 points
correlation = 0.06151, correlation about mean = 0.01585, overlap = 7667
steps = 1272, shift = 23.2, angle = 26.1 degrees
Position of cryosparc_P27_J169_006_volume_map_sharp.mrc (#7) relative to
denmod_map_sharpened.ccp4 (#4) coordinates:
Matrix rotation and translation
0.93221597 0.34573317 0.10696713 -52.27512127
-0.30530050 0.90999317 -0.28054241 128.56452027
-0.19433218 0.22886899 0.95386267 10.71782266
Axis 0.57897899 0.34244615 -0.73994186
Axis point 347.05485705 229.00652377 -0.00000000
Rotation angle (degrees) 26.09891589
Shift along axis 5.82966208
> fitmap #7 inMap #4
Fit map cryosparc_P27_J169_006_volume_map_sharp.mrc in map
denmod_map_sharpened.ccp4 using 166885 points
correlation = 0.06151, correlation about mean = 0.01585, overlap = 7667
steps = 44, shift = 0.0043, angle = 0.0047 degrees
Position of cryosparc_P27_J169_006_volume_map_sharp.mrc (#7) relative to
denmod_map_sharpened.ccp4 (#4) coordinates:
Matrix rotation and translation
0.93222485 0.34568859 0.10703374 -52.27990730
-0.30523991 0.91001126 -0.28054965 128.54828464
-0.19438473 0.22886439 0.95385307 10.73026552
Axis 0.57900534 0.34259540 -0.73985215
Axis point 347.06823586 229.04611214 0.00000000
Rotation angle (degrees) 26.09778413
Shift along axis 5.83089479
> select add #7
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.84486,0.50163,0.18594,198.87,0.45868,0.85809,-0.23086,4.1683,-0.27536,-0.10976,-0.95506,397.67
> fitmap #7 inMap #4
Fit map cryosparc_P27_J169_006_volume_map_sharp.mrc in map
denmod_map_sharpened.ccp4 using 166885 points
correlation = 0.0594, correlation about mean = 0.01871, overlap = 7496
steps = 188, shift = 5.65, angle = 5.88 degrees
Position of cryosparc_P27_J169_006_volume_map_sharp.mrc (#7) relative to
denmod_map_sharpened.ccp4 (#4) coordinates:
Matrix rotation and translation
-0.86231574 0.49040453 0.12615453 219.28647055
0.43602383 0.84578589 -0.30745642 21.97255882
-0.25747774 -0.21011813 -0.94316254 410.05363265
Axis 0.24364611 0.96026457 -0.13611957
Axis point 128.53133958 0.00000000 195.30361365
Rotation angle (degrees) 168.47745940
Shift along axis 18.71144284
> hide #!3 models
> fitmap #7 inMap #4
Fit map cryosparc_P27_J169_006_volume_map_sharp.mrc in map
denmod_map_sharpened.ccp4 using 166885 points
correlation = 0.0594, correlation about mean = 0.0187, overlap = 7496
steps = 52, shift = 0.0135, angle = 0.00384 degrees
Position of cryosparc_P27_J169_006_volume_map_sharp.mrc (#7) relative to
denmod_map_sharpened.ccp4 (#4) coordinates:
Matrix rotation and translation
-0.86230764 0.49042195 0.12614213 219.27908285
0.43602666 0.84576183 -0.30751858 21.99882737
-0.25750006 -0.21017429 -0.94314393 410.06109767
Axis 0.24365321 0.96025821 -0.13615168
Axis point 128.52557476 0.00000000 195.30966937
Rotation angle (degrees) 168.47708031
Shift along axis 18.72210149
> fitmap #7 inMap #4
Fit map cryosparc_P27_J169_006_volume_map_sharp.mrc in map
denmod_map_sharpened.ccp4 using 166885 points
correlation = 0.05939, correlation about mean = 0.01871, overlap = 7495
steps = 44, shift = 0.00804, angle = 0.00434 degrees
Position of cryosparc_P27_J169_006_volume_map_sharp.mrc (#7) relative to
denmod_map_sharpened.ccp4 (#4) coordinates:
Matrix rotation and translation
-0.86228520 0.49047103 0.12610473 219.27714779
0.43609056 0.84573900 -0.30749075 21.98402640
-0.25746699 -0.21015164 -0.94315801 410.05990816
Axis 0.24368352 0.96025236 -0.13613873
Axis point 128.52222951 0.00000000 195.30995951
Rotation angle (degrees) 168.47915493
Shift along axis 18.71940442
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.86229,0.49047,0.1261,219.51,0.43609,0.84574,-0.30749,84.181,-0.25747,-0.21015,-0.94316,411.22
> volume #7 level 0.3677
> view matrix models
> #7,-0.86229,0.49047,0.1261,220.11,0.43609,0.84574,-0.30749,41.584,-0.25747,-0.21015,-0.94316,429.72
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.44955,0.8812,0.14625,82.208,0.88717,0.4214,0.188,-52.316,0.10403,0.21427,-0.97122,303.45
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.44955,0.8812,0.14625,98.647,0.88717,0.4214,0.188,-58.525,0.10403,0.21427,-0.97122,309.96
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.98035,-0.18708,0.062535,381.95,-0.18148,0.97965,0.08569,43.074,-0.077293,0.072658,-0.99436,368.09
> fitmap #7 inMap #4
Fit map cryosparc_P27_J169_006_volume_map_sharp.mrc in map
denmod_map_sharpened.ccp4 using 59750 points
correlation = 0.8166, correlation about mean = 0.7146, overlap = 1.302e+05
steps = 196, shift = 9.02, angle = 4.99 degrees
Position of cryosparc_P27_J169_006_volume_map_sharp.mrc (#7) relative to
denmod_map_sharpened.ccp4 (#4) coordinates:
Matrix rotation and translation
-0.96337451 -0.26143316 0.05968457 394.25444951
-0.25198447 0.95868843 0.13198598 56.27998048
-0.09172442 0.11211235 -0.98945310 357.10416222
Axis -0.12989327 0.98960291 0.06175621
Axis point 207.70059055 0.00000000 169.09878686
Rotation angle (degrees) 175.61259380
Shift along axis 26.53723447
> hide #!4 models
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/Phenixjobs/LocalAnisoSharpen_50/denmod_map_sharpened.ccp4
Opened denmod_map_sharpened.ccp4 as #8, grid size 256,256,256, pixel 1.33,
shown at level 0.0194, step 1, values float32
> surface dust #7 size 13.3
[Repeated 1 time(s)]
> ui mousemode right select
> select clear
> surface dust #7 size 13.3
> surface dust #8 size 13.3
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> select add #8
2 models selected
> view matrix models
> #8,-0.99502,-0.022188,-0.097177,349.75,-0.0058498,0.98623,-0.16528,32.958,0.099506,-0.16389,-0.98145,366.97
> volume #8 level 0.06246
> volume #8 level 0.0883
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.99502,-0.022188,-0.097177,384.28,-0.0058498,0.98623,-0.16528,62.051,0.099506,-0.16389,-0.98145,363.47
> fitmap #8 inMap #4
Fit map denmod_map_sharpened.ccp4 in map denmod_map_sharpened.ccp4 using 42839
points
correlation = 0.169, correlation about mean = 0.04852, overlap = 5061
steps = 84, shift = 8.1, angle = 9.11 degrees
Position of denmod_map_sharpened.ccp4 (#8) relative to
denmod_map_sharpened.ccp4 (#4) coordinates:
Matrix rotation and translation
-0.99881070 -0.04655374 -0.01448952 372.17981273
-0.04602945 0.99833973 -0.03462776 47.87384321
0.01607752 -0.03391963 -0.99929524 365.18154099
Axis 0.02315677 -0.99958482 0.01714496
Axis point 185.24572029 0.00000000 184.42757812
Rotation angle (degrees) 179.12392082
Shift along axis -32.97446086
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.9239,-0.37984,0.046241,405.37,-0.37534,0.92312,0.083433,93.157,-0.074377,0.059727,-0.99544,363.43
> fitmap #8 inMap #4
Fit map denmod_map_sharpened.ccp4 in map denmod_map_sharpened.ccp4 using 42839
points
correlation = 0.8488, correlation about mean = 0.7106, overlap = 3.92e+04
steps = 120, shift = 5.05, angle = 8.21 degrees
Position of denmod_map_sharpened.ccp4 (#8) relative to
denmod_map_sharpened.ccp4 (#4) coordinates:
Matrix rotation and translation
-0.96355072 -0.26040696 0.06130437 393.94566458
-0.24975150 0.95772978 0.14275108 53.27419604
-0.09588639 0.12223705 -0.98785825 355.03080297
Axis -0.12911538 0.98935910 0.06706551
Axis point 207.55258024 0.00000000 167.72266940
Rotation angle (degrees) 175.44358218
Shift along axis 25.65319127
> hide #!7 models
> show #!4 models
> color #4 #fe3128ff models
> fitmap #8 inMap #4
Fit map denmod_map_sharpened.ccp4 in map denmod_map_sharpened.ccp4 using 42839
points
correlation = 0.8488, correlation about mean = 0.7107, overlap = 3.92e+04
steps = 48, shift = 0.0274, angle = 0.0216 degrees
Position of denmod_map_sharpened.ccp4 (#8) relative to
denmod_map_sharpened.ccp4 (#4) coordinates:
Matrix rotation and translation
-0.96356137 -0.26035520 0.06135683 393.93364244
-0.24972937 0.95779041 0.14238253 53.33863345
-0.09583702 0.12187170 -0.98790818 355.06800208
Axis -0.12909468 0.98937445 0.06687874
Axis point 207.55091153 0.00000000 167.74446357
Rotation angle (degrees) 175.44356318
Shift along axis 25.66364347
> ui mousemode right select
> select clear
> volume #8 level 0.06196
> select clear
> ui mousemode right translate
> volume #4 level 0.3733
> hide #!4 models
> show #!4 models
> hide #!8 models
> show #!8 models
> hide #!4 models
> show #!7 models
> volume #7 level 0.2873
> hide #!7 models
> hide #!8 models
> show #1 models
> hide #1 models
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/refit_AP2Nef_rigid_body_081325.pdb
Chain information for refit_AP2Nef_rigid_body_081325.pdb #9
---
Chain | Description
A | No description available
B | No description available
M | No description available
N | No description available
S | No description available
> hide #!9,12 atoms
> show #!9,12 cartoons
> ui tool show Matchmaker
> matchmaker #!9 to #12
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 bestfit_AP2Nef_03032025.pdb, chain A (#12) with
refit_AP2Nef_rigid_body_081325.pdb, chain A (#9), sequence alignment score =
3131.6
RMSD between 612 pruned atom pairs is 0.621 angstroms; (across all 612 pairs:
0.621)
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/cryosparc_P27_J141_flex_map.mrc
Opened cryosparc_P27_J141_flex_map.mrc as #10, grid size 256,256,256, pixel
1.33, shown at level 0.00547, step 1, values float32
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> select add #12
23313 atoms, 23539 bonds, 1 pseudobond, 1575 residues, 2 models selected
> select subtract #12
Nothing selected
> select add #10
2 models selected
> view matrix models
> #10,-0.39019,-0.69891,-0.5994,455.04,-0.9207,0.30185,0.24738,242.94,0.0080308,0.64839,-0.76126,157.38
> ui mousemode right "translate selected models"
> view matrix models
> #10,-0.39019,-0.69891,-0.5994,460.98,-0.9207,0.30185,0.24738,235.81,0.0080308,0.64839,-0.76126,185.1
> fitmap #10 inMap #3
Fit map cryosparc_P27_J141_flex_map.mrc in map
cryosparc_P27_J86_004_volume_map.mrc using 167754 points
correlation = 0.5481, correlation about mean = 0.08194, overlap = 363
steps = 536, shift = 44, angle = 55.7 degrees
Position of cryosparc_P27_J141_flex_map.mrc (#10) relative to
cryosparc_P27_J86_004_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.86304810 -0.29729772 0.40836522 5.51564204
-0.27539802 0.40077578 0.87380478 6.33841640
-0.42344303 -0.86659850 0.26401355 367.07140409
Axis -0.90218875 0.43119204 0.01135235
Axis point 0.00000000 271.04666949 179.56980595
Rotation angle (degrees) 74.69728821
Shift along axis 1.92404664
> show #!3 models
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.68737,0.69846,-0.19918,-5.8329,0.71705,-0.69623,0.033076,202.28,-0.11557,-0.16555,-0.97941,386.95
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.68737,0.69846,-0.19918,-9.1264,0.71705,-0.69623,0.033076,205.6,-0.11557,-0.16555,-0.97941,412.77
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.97629,0.035855,-0.21348,393.65,-0.017714,0.96965,0.24387,-5.6057,0.21574,0.24187,-0.94602,277.84
> fitmap #10 inMap #3
Fit map cryosparc_P27_J141_flex_map.mrc in map
cryosparc_P27_J86_004_volume_map.mrc using 167754 points
correlation = 0.9937, correlation about mean = 0.969, overlap = 920
steps = 196, shift = 2.31, angle = 24.1 degrees
Position of cryosparc_P27_J141_flex_map.mrc (#10) relative to
cryosparc_P27_J86_004_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99998432 0.00265206 0.00494389 -1.40155691
-0.00263801 0.99999252 -0.00284351 0.99648980
-0.00495139 0.00283041 0.99998379 0.32244093
Axis 0.45125783 0.78699004 -0.42072918
Axis point 65.55297294 0.00000000 285.17160653
Rotation angle (degrees) 0.36020857
Shift along axis 0.01610372
> select subtract #10
Nothing selected
> show #1 models
> select add #1
5971 atoms, 6096 bonds, 620 residues, 1 model selected
> hide #!9 models
> show #!9 models
> hide #!10 models
> hide #!12 models
> ui mousemode right "rotate selected models"
> ui mousemode right select
> hide #1 models
> show #1 models
> hide #1 models
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/alphafold_predictions/fold_2025_02_09_18_49_serinc5/fold_2025_02_09_18_49_serinc5_model_4.cif
Chain information for fold_2025_02_09_18_49_serinc5_model_4.cif #11
---
Chain | Description
A | .
> show #11#!9 cartoons
[Repeated 2 time(s)]
> select add #11
9719 atoms, 9945 bonds, 1100 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.072227,0.96932,0.23494,262.17,0.16703,-0.22048,0.96098,352.3,0.9833,0.10865,-0.14598,470.88,#11,1,0,0,59.169,0,1,0,154.38,0,0,1,236.3
> view matrix models
> #1,-0.072227,0.96932,0.23494,391.72,0.16703,-0.22048,0.96098,443.1,0.9833,0.10865,-0.14598,526.47,#11,1,0,0,188.72,0,1,0,245.17,0,0,1,291.89
> ui mousemode right translate
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.80621,0.57075,0.15578,119.41,-0.58388,-0.72509,-0.36515,-102.88,-0.095455,-0.38535,0.91782,379.66,#11,0.64807,-0.11079,-0.75348,186.53,-0.74646,-0.28857,-0.5996,246.42,-0.151,0.95103,-0.26972,285.36
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.80621,0.57075,0.15578,114.65,-0.58388,-0.72509,-0.36515,-129.4,-0.095455,-0.38535,0.91782,347.45,#11,0.64807,-0.11079,-0.75348,181.76,-0.74646,-0.28857,-0.5996,219.9,-0.151,0.95103,-0.26972,253.14
> view matrix models
> #1,-0.80621,0.57075,0.15578,123.41,-0.58388,-0.72509,-0.36515,-131.23,-0.095455,-0.38535,0.91782,346.71,#11,0.64807,-0.11079,-0.75348,190.53,-0.74646,-0.28857,-0.5996,218.07,-0.151,0.95103,-0.26972,252.4
> view matrix models
> #1,-0.80621,0.57075,0.15578,122.75,-0.58388,-0.72509,-0.36515,-132.19,-0.095455,-0.38535,0.91782,342.65,#11,0.64807,-0.11079,-0.75348,189.87,-0.74646,-0.28857,-0.5996,217.11,-0.151,0.95103,-0.26972,248.34
> ui mousemode right select
> select clear
> color #11 #4c5ba7ff
> hide #!9 models
> hide #11 models
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/comparison_processing_2024_2025.cxs
> includeMaps true
——— End of log from Mon Aug 18 17:27:18 2025 ———
opened ChimeraX session
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!9 models
> volume #5 level 0.8454
> hide #!5 models
> volume #3 level 0.1124
> show #11 models
> volume #3 level 0.1098
> color #3 #c0a3cbc8 models
> color #3 #c0a3cbb3 models
> select #9/N
2218 atoms, 2255 bonds, 1 pseudobond, 135 residues, 2 models selected
> color #9 #29b5c4ff
> color #9 #32ddf0ff
> graphics silhouettes false
> graphics silhouettes true
> select #9/B
8235 atoms, 8301 bonds, 564 residues, 1 model selected
> color sel red
> select #9/A
8924 atoms, 9002 bonds, 612 residues, 1 model selected
> color sel magenta
> select #9/S
2218 atoms, 2242 bonds, 140 residues, 1 model selected
> color sel orange
> select #9/M
1839 atoms, 1860 bonds, 124 residues, 1 model selected
> color sel lime
> ui mousemode right select
> select clear
> volume #3 color #c0a3cb92
> volume #3 color #c0a3cb91
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/CSp27_j86_structureoverlay.png
> width 1528 height 804 supersample 1 transparentBackground true
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> show #!7 models
> volume #7 level 0.2603
> volume #7 level 0.3815
> hide #!7 models
> show #!8 models
> volume #8 level 0.1043
> hide #11 models
> show #11 models
> hide #11 models
> show #!10 models
> hide #!10 models
> show #!7 models
> hide #!8 models
> volume #7 level 0.4757
> hide #!7 models
> show #!4 models
> volume #4 level 1.322
> volume #4 level 1.223
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!8 models
> volume #8 level 0.0884
> hide #!9 models
> show #!7 models
> volume #7 level 0.4891
> hide #!8 models
> show #!9 models
> volume #7 level 0.4084
> show #!4 models
> hide #!7 models
> hide #!4 models
> show #!8 models
> hide #!8 models
> show #!7 models
> volume #7 level 0.7313
> show #!2 models
> hide #!7 models
> show #11 models
> volume #2 level 0.6761
> volume #2 level 1.075
> show #!7 models
> volume #7 level 0.516
> hide #!7 models
> volume #2 level 0.7616
> show #!4 models
> hide #!2 models
> color #4 #acffd8ff models
> color #4 #acffd877 models
> color #4 #acffd878 models
> volume #4 level 1.372
> hide #!4 models
> show #!2 models
> volume #2 level 1.816
> hide #!2 models
> show #!8 models
> volume #8 level 0.1148
> color #8 #b2ffff81 models
> color #8 #b2ffff82 models
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/comparison_processing_2024_2025.cxs
> includeMaps true
——— End of log from Thu Sep 18 21:45:21 2025 ———
opened ChimeraX session
> hide #!8 models
> hide #!9 models
> hide #11 models
> show #!2 models
> color #2 #c8c9cbff models
> volume #2 level 1.246
> volume #2 level 1.047
> volume #2 level 0.9896
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/cs_p24_j249_resampled_sharp.png
> width 1026 height 858 supersample 1 transparentBackground true
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/bestfit_AP2nef_08122025.pdb
Chain information for bestfit_AP2nef_08122025.pdb #13
---
Chain | Description
A | No description available
B | No description available
M | No description available
N | No description available
S | No description available
> hide #!13 atoms
> show #!13 cartoons
> ui tool show Matchmaker
> matchmaker #!13 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker refit_AP2Nef_rigid_body_081325.pdb, chain A (#9) with
bestfit_AP2nef_08122025.pdb, chain A (#13), sequence alignment score = 3150.8
RMSD between 612 pruned atom pairs is 0.591 angstroms; (across all 612 pairs:
0.591)
> color #2 #c8c9cb85 models
> select #13?a
Expected an objects specifier or a keyword
> select #13/A
8924 atoms, 9002 bonds, 612 residues, 1 model selected
> color sel blue
> color sel cyan
> select #13/B
8188 atoms, 8254 bonds, 564 residues, 1 model selected
> ui tool show "Color Actions"
> color sel chartreuse
> select #13/N
2218 atoms, 2255 bonds, 1 pseudobond, 135 residues, 2 models selected
> ui tool show "Color Actions"
> color sel yellow
> select #13/S
2218 atoms, 2242 bonds, 140 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light coral
> select #13/M
1839 atoms, 1860 bonds, 124 residues, 1 model selected
> color sel magenta
> hide #!13 models
> volume #2 level 0.8471
> color #2 #c8c9cbff models
> volume #2 level 0.9041
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/cs_p24_j249_resampled_sharp.png
> width 1026 height 858 supersample 1 transparentBackground true
> show #!13 models
> hide #!13 models
> show #!13 models
> color #2 #c8c9cb7b models
> color #2 #c8c9cb7a models
> volume #2 level 0.8471
> select add #13
23387 atoms, 23613 bonds, 1 pseudobond, 1575 residues, 2 models selected
> select subtract #13
Nothing selected
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/cs_p24_j249_resampled_sharp_with_model.png
> width 1026 height 858 supersample 1 transparentBackground true
> hide #!2 models
> show #!3 models
> hide #!13 models
> hide #!3 models
> show #!5 models
> volume #5 level 0.6962
> hide #!5 models
> show #!3 models
> volume #3 level 0.1278
> show #!5 models
> volume #3 level 0.1073
> hide #!5 models
> show #!10 models
> hide #!10 models
> show #!5 models
> hide #!3 models
> hide #!5 models
> show #!3 models
> volume #3 level 0.1021
> show #!13 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #11 models
> hide #11 models
> hide #!13 models
> show #!5 models
> hide #!3 models
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/cs_p24_j221_consensus_map.png
> width 1026 height 858 supersample 1 transparentBackground true
> hide #!5 models
> show #!3 models
> ui tool show "Map Eraser"
> volume erase #3 center 211.62,245.62,252.37 radius 13.3
> volume erase #3 center 227.63,226.57,251.49 radius 13.3
> volume erase #3 center 225.83,225.34,258.13 radius 13.3
> volume erase #3 center 217.71,207.29,267.53 radius 13.3
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/cs_p27_j86_refined_vol.png
> width 1026 height 858 supersample 1 transparentBackground true
> show #!13 models
> show #11 models
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/cs_p27_j86_refined_vol_overlay_map.png
> width 1026 height 858 supersample 1 transparentBackground true
> hide #!3 models
> hide #11 models
> open "/Users/joanapaulino/Documents/postdoc_UCSF/Serinc/Nef_AP2
> structures/Nef_AP2_noTet.pdb"
Chain information for Nef_AP2_noTet.pdb #14
---
Chain | Description
A | No description available
B | No description available
M | No description available
N | No description available
S | No description available
> hide #!13-14 atoms
> show #!13-14 cartoons
> ui tool show Matchmaker
> matchmaker #!14 to #13
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 bestfit_AP2nef_08122025.pdb, chain A (#13) with Nef_AP2_noTet.pdb,
chain A (#14), sequence alignment score = 2886.3
RMSD between 275 pruned atom pairs is 1.074 angstroms; (across all 590 pairs:
5.445)
> matchmaker #!14 to #13
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 bestfit_AP2nef_08122025.pdb, chain A (#13) with Nef_AP2_noTet.pdb,
chain A (#14), sequence alignment score = 2886.3
RMSD between 275 pruned atom pairs is 1.074 angstroms; (across all 590 pairs:
5.445)
> show #!12 models
> hide #!13 models
> show #!13 models
> hide #!12 models
> hide #!13 models
> show #!7 models
> hide #!14 models
> color #7 #ffffb282 models
> graphics silhouettes false
> graphics silhouettes true
> show #!2 models
> show #!13 models
> hide #!7 models
> show #!13 surfaces
> hide #!13 surfaces
> show #!13 atoms
> show #!7 models
> volume #7 level 0.3815
> hide #!7 models
> hide #!2 models
> show #!2 models
> show #!7 models
> hide #!2 models
> volume #7 level 0.6237
> hide #!7 models
> show #!2 models
> hide #!13 atoms
> hide #!13 cartoons
> show #!13 surfaces
> color #2 #c8c9cbff models
> color #2 #c8c9cb9c models
> color #2 #c8c9cba3 models
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/cs_p24_j249_resampled_sharp_with_modelvolume.png
> width 1026 height 858 supersample 1 transparentBackground true
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/cs_p24_j249_resampled_sharp_with_modelvolume_zoom.png
> width 1026 height 858 supersample 1 transparentBackground true
> select #13/S:97,99
22 atoms, 20 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 22 atom styles
> style sel stick
Changed 22 atom styles
> transparency sel 50
> style sel sphere
Changed 22 atom styles
> style sel sphere
Changed 22 atom styles
> transparency sel 0
> transparency sel 50
> transparency sel 0
> transparency sel 50
> transparency sel 0
> transparency sel 50
> style sel ball
Changed 22 atom styles
> ui tool show "Color Actions"
> color sel red
> color sel byelement
> select add #13
23387 atoms, 23613 bonds, 1 pseudobond, 1575 residues, 3 models selected
> select subtract #13
5 models selected
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/cs_p24_j249_resampled_sharp_with_modelvolume_zoom_topview_cys.png
> width 1026 height 858 supersample 3
> hide #!2 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
Alignment identifier is 4
Alignment identifier is 5
Alignment identifier is 6
Alignment identifier is 7
Alignment identifier is 8
Alignment identifier is 9
Alignment identifier is 10
> select #6/S:1-45 #14/S:1-45
708 atoms, 718 bonds, 90 residues, 2 models selected
> select #6/S:1-45 #14/S:1-45
708 atoms, 718 bonds, 90 residues, 2 models selected
5 [ID: 5] region 2 chains [1-45] RMSD: 1.019
> ui tool show "Model Panel"
> select add #14
11929 atoms, 12155 bonds, 1 pseudobond, 1610 residues, 3 models selected
> select subtract #14
354 atoms, 359 bonds, 45 residues, 1 model selected
> select add #13
23741 atoms, 23972 bonds, 1 pseudobond, 1620 residues, 3 models selected
> select subtract #13
354 atoms, 359 bonds, 45 residues, 6 models selected
> select add #13
23741 atoms, 23972 bonds, 1 pseudobond, 1620 residues, 3 models selected
> select add #6
34962 atoms, 35409 bonds, 2 pseudobonds, 3140 residues, 9 models selected
> select subtract #6
23387 atoms, 23613 bonds, 1 pseudobond, 1575 residues, 7 models selected
Alignment identifier is 13/A
Alignment identifier is 13/B
Alignment identifier is 13/M
Alignment identifier is 13/S
Alignment identifier is 13/N
> select #13/S:68
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #13/S:68-69
30 atoms, 29 bonds, 2 residues, 1 model selected
> select #13/S:70-71
27 atoms, 26 bonds, 2 residues, 1 model selected
> select #13/S:69-71
46 atoms, 45 bonds, 3 residues, 1 model selected
> select #13/S:4-9,14-19,58-62,65-69
420 atoms, 423 bonds, 22 residues, 1 model selected
> select #13/S:68
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #13/S:68-71
57 atoms, 56 bonds, 4 residues, 1 model selected
> select #13/S:70
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #13/S:70
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #13/S:69-70
30 atoms, 29 bonds, 2 residues, 1 model selected
> select #13/S:68-70
41 atoms, 40 bonds, 3 residues, 1 model selected
> select #13/S:97
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #13/S:97-101
72 atoms, 71 bonds, 5 residues, 1 model selected
> ui mousemode right select
> select clear
> show #!2 models
> hide #!2 models
> ui mousemode right swapaa
> swapaa mousemode #13/S:97 CYS
> ui mousemode right swapaa
> swapaa mousemode #13/S:97 CYS
> swapaa #13/S:97 asn
Using Dunbrack library
bestfit_AP2nef_08122025.pdb #13/S CYS 97: phi 56.7, psi 18.5 trans
Density criteria with multiple volume models open;
Need to specify one to use via 'density' keyword.
> hide #!13 atoms
[Repeated 1 time(s)]
> hide #!13 surfaces
> show #!13 atoms
> swapaa #13/S:97 asn
Using Dunbrack library
bestfit_AP2nef_08122025.pdb #13/S CYS 97: phi 56.7, psi 18.5 trans
Density criteria with multiple volume models open;
Need to specify one to use via 'density' keyword.
> swapaa #13/S:97 asn density #2
Using Dunbrack library
bestfit_AP2nef_08122025.pdb #13/S CYS 97: phi 56.7, psi 18.5 trans
Applying ASN rotamer (chi angles: 63.8 -26.4) to bestfit_AP2nef_08122025.pdb
#13/S ASN 97
> show #!2 models
> ui mousemode right select
> select #13/S:97@CG
1 atom, 1 residue, 1 model selected
> ui mousemode right swapaa
> swapaa #13/S:97
Missing or invalid "resTypes" argument: Expected a text string
> hide sel atoms
[Repeated 1 time(s)]
> show sel cartoons
> select add #13
23386 atoms, 23612 bonds, 1 pseudobond, 1575 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> hide #!2 models
> ui mousemode right select
> select clear
> select #13/S:97
10 atoms, 9 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!2 models
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
Chain information for bestfit_AP2nef_08122025.pdb
---
Chain | Description
13.2/A | No description available
13.2/B | No description available
13.2/M | No description available
13.2/N | No description available
13.2/S | No description available
Drag select of 1 atoms
Drag select of 2 cryosparc_P24_J249_010_volume_map_sharp_resampled.mrc , 1
atoms, 1 residues, 1 bonds
> isolde sim start #13.2/S:97
Sim termination reason: None
ISOLDE: stopped sim
> isolde sim start #13.2/S:97
Sim termination reason: None
ISOLDE: stopped sim
> isolde sim start #13.2/S:97
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> clipper associate #2 toModel #13
Opened cryosparc_P24_J249_010_volume_map_sharp_resampled.mrc as #13.1.1.1,
grid size 97,111,122, pixel 1.24,1.24,1.24, shown at step 1, values float32
> isolde sim start #13.2/S:94-100
ISOLDE: started sim
> isolde sim pause
3 models selected
[Repeated 3 time(s)]
> ui mousemode right select
> select clear
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Volume Viewer"
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/bestfit_AP2nef_110325.pdb
> models #13
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/comparison_processing_2024_2025.cxs
> includeMaps true
——— End of log from Mon Nov 3 11:46:56 2025 ———
opened ChimeraX session
> close #13
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/bestfit_AP2nef_110325.pdb
Chain information for bestfit_AP2nef_110325.pdb #2
---
Chain | Description
A | No description available
B | No description available
M | No description available
N | No description available
S | No description available
> hide #!2 atoms
> show #!2 cartoons
> show #!12 models
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/cryosparc_P27_J169_006_volume_map_sharp.mrc
Opened cryosparc_P27_J169_006_volume_map_sharp.mrc as #13, grid size
256,256,256, pixel 1.33, shown at level 0.159, step 1, values float32
> hide #!13 models
> show #!13 models
> close #13
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/comparison_processing_2024_2025.cxs
> includeMaps true
——— End of log from Mon Nov 3 11:59:03 2025 ———
opened ChimeraX session
> open
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/cryosparc_P24_J249_010_volume_map_sharp_resampled.mrc
Opened cryosparc_P24_J249_010_volume_map_sharp_resampled.mrc as #13, grid size
97,111,122, pixel 1.24,1.24,1.24, shown at level 2.47, step 1, values float32
> color #13 #b2b2b28a models
> volume #13 level 0.679
> surface dust #13 size 12.4
> volume #13 level 1.192
> volume #13 level 1.278
> volume #13 level 0.8786
> hide #!13 models
> select #2/A
8924 atoms, 9002 bonds, 612 residues, 1 model selected
> color sel cyan
> select #2/B
8188 atoms, 8254 bonds, 564 residues, 1 model selected
> ui tool show "Color Actions"
> color sel chartreuse
> color sel lime
> color sel chartreuse
> select #2/M
1839 atoms, 1860 bonds, 124 residues, 1 model selected
> color sel magenta
> select #2/S
2221 atoms, 2245 bonds, 140 residues, 1 model selected
> ui tool show "Color Actions"
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!14 models
> hide #!14 models
> show #!14 models
> show #!6 models
> hide #!14 models
> hide #!6 models
> ui tool show "Color Actions"
> color sel light coral
> select #2/N
2218 atoms, 2255 bonds, 1 pseudobond, 135 residues, 2 models selected
> color (#!2 & sel) yellow
> ui mousemode right select
> select clear
> show #!13 models
> select add #2
23390 atoms, 23616 bonds, 1 pseudobond, 1575 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> hide sel cartoons
> show sel atoms
> hide sel atoms
> hide sel surfaces
> show sel surfaces
> select #2/S:97
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel surfaces
> show sel atoms
> style sel sphere
Changed 14 atom styles
> style sel stick
Changed 14 atom styles
> color (#!2 & sel) byelement
> select #2/S:99
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel surfaces
> show sel atoms
> style sel ball
Changed 11 atom styles
> color (#!2 & sel) byelement
> select clear
> select #2/S:99
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel ball
Changed 11 atom styles
> style sel sphere
Changed 11 atom styles
> style sel ball
Changed 11 atom styles
> select clear
> volume #13 level 0.8786
> select #2/S:97
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel surfaces
[Repeated 1 time(s)]
> ui tool show "Color Actions"
> color sel light coral
> select clear
Drag select of bestfit_AP2nef_110325.pdb_N SES surface, 221 of 211812
triangles, bestfit_AP2nef_110325.pdb_S SES surface, 136 of 192552 triangles,
13 cryosparc_P24_J249_010_volume_map_sharp_resampled.mrc
> select clear
> hide #!13 models
> hide #!2 surfaces
> show #!2 cartoons
> select #2/N:166
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 14 atom styles
> show #!13 models
> hide #!13 models
> select #2/N:165
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 14 atom styles
> show #!13 models
> show sel surfaces
[Repeated 1 time(s)]
> select #13
2 models selected
> show #!2 surfaces
> select clear
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/cs_p24_j249_resampled_sharp_with_modelvolume.png
> width 1749 height 1129 supersample 2 transparentBackground true
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/cs_p24_j249_resampled_sharp_with_modelvolume_zoom.png
> width 1749 height 1129 supersample 2 transparentBackground true
> select #2/S:99
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel surfaces
> ui tool show "Color Actions"
> color sel light coral
> color (#!2 & sel) byhetero
> select clear
> hide #!13 models
> show #!13 models
> hide #!13 models
> select #2/S:105
20 atoms, 20 bonds, 1 residue, 1 model selected
> hide sel surfaces
> show sel atoms
> style sel ball
Changed 20 atom styles
> color (#!2 & sel) byhetero
> show #!13 models
> hide #!13 models
> select #2/S:102
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel surfaces
> style sel ball
Changed 12 atom styles
> style sel ball
Changed 12 atom styles
> show sel atoms
> color (#!2 & sel) byhetero
> show #!13 models
> select clear
> select #2/N:165
14 atoms, 13 bonds, 1 residue, 1 model selected
> hide sel surfaces
> show sel atoms
> style sel ball
Changed 14 atom styles
> color (#!2 & sel) byhetero
> select clear
> hide #!13 models
> select #2/S:101
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel surfaces
> show sel atoms
> style sel ball
Changed 19 atom styles
> color (#!2 & sel) byhetero
> select clear
> show #!13 models
> select #2/S:101
19 atoms, 18 bonds, 1 residue, 1 model selected
> color (#!2 & sel) byelement
> hide #!13 models
> select #2/S:105,102,99
43 atoms, 41 bonds, 3 residues, 1 model selected
> color (#!2 & sel) byelement
> select #2/N:165
14 atoms, 13 bonds, 1 residue, 1 model selected
> color (#!2 & sel) byelement
> select clear
> show #!13 models
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/cs_p24_j249_resampled_sharp_with_modelvolume_zoom_topview_contacts.png
> width 1749 height 1129 supersample 1 transparentBackground true
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/cs_p24_j249_resampled_sharp_with_modelvolume_zoom_topview_contacts_v2.png
> width 1749 height 1129 supersample 1 transparentBackground true
> hide #!13 models
> show #!13 models
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/cs_p24_j249_resampled_sharp_with_modelvolume_zoom_topview_contacts_profile.png
> width 1749 height 1129 supersample 1 transparentBackground true
> hide #!2 models
> hide #!13 models
> show #1 models
> show #1 cartoons
> show #!13 models
> hide #1 models
> show #1 models
> hide #1 models
> show #!2 models
> select clear
[Repeated 2 time(s)]
> cofr frontCenter
> select clear
> show #11 models
> hide #!13 models
> hide #!2 models
Drag select of 2 residues
> select clear
> select #11:344-392
387 atoms, 396 bonds, 49 residues, 1 model selected
> color sel cyan
> select clear
> select #11:346
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 11 atom styles
> select clear
> select #11:352
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 8 atom styles
> select #11:366-368
24 atoms, 23 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 24 atom styles
> select clear
> show #!6 models
> hide #!6 models
> show #!13 models
> show #!2 models
> show #!3 models
> volume #3 level 0.2407
> select add #11
3748 atoms, 3849 bonds, 480 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.64807,-0.11079,-0.75348,195.91,-0.74646,-0.28857,-0.5996,208.77,-0.151,0.95103,-0.26972,250.6
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.88247,0.092663,0.46115,200.04,0.44567,0.14875,-0.88275,204.59,-0.15039,0.98452,0.089968,252
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.88247,0.092663,0.46115,188.55,0.44567,0.14875,-0.88275,201.57,-0.15039,0.98452,0.089968,252.87
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.24826,-0.41178,0.87682,193.27,0.83341,0.37057,0.41,205.69,-0.49375,0.83254,0.25118,254.45
> view matrix models
> #11,-0.3734,-0.13114,0.91835,193.19,0.72243,0.57991,0.37656,205.4,-0.58195,0.80406,-0.1218,253.15
> view matrix models
> #11,-0.5057,-0.22411,0.83309,193.25,0.53559,0.67548,0.50682,206.12,-0.67632,0.7025,-0.22156,253.1
> hide #!3 models
> view matrix models
> #11,-0.73922,-0.59528,0.31495,192.24,-0.09467,0.55486,0.82654,208.83,-0.66677,0.58118,-0.46652,252.3
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.73922,-0.59528,0.31495,191.69,-0.09467,0.55486,0.82654,209.03,-0.66677,0.58118,-0.46652,254.78
> view matrix models
> #11,-0.73922,-0.59528,0.31495,191,-0.09467,0.55486,0.82654,208.89,-0.66677,0.58118,-0.46652,253.84
> view matrix models
> #11,-0.73922,-0.59528,0.31495,191.52,-0.09467,0.55486,0.82654,208.96,-0.66677,0.58118,-0.46652,253.55
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.88862,-0.41984,0.18465,190.97,-0.10918,0.58466,0.8039,208.85,-0.44547,0.6942,-0.56538,252.53
> view matrix models
> #11,-0.85479,-0.46923,0.22172,191.14,-0.10632,0.57649,0.81015,208.88,-0.50797,0.66894,-0.54267,252.79
> view matrix models
> #11,-0.90186,-0.39796,0.16815,190.89,-0.11019,0.58823,0.80115,208.83,-0.41773,0.704,-0.57435,252.43
> view matrix models
> #11,0.51397,0.49705,0.69913,188.79,0.82537,-0.064561,-0.56088,202.67,-0.23365,0.86532,-0.44343,252.33
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.51397,0.49705,0.69913,203.91,0.82537,-0.064561,-0.56088,201.71,-0.23365,0.86532,-0.44343,259.39
> view matrix models
> #11,0.51397,0.49705,0.69913,203.27,0.82537,-0.064561,-0.56088,202.78,-0.23365,0.86532,-0.44343,252.8
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.52663,0.49904,0.6882,203.2,0.81648,-0.071517,-0.57293,202.76,-0.2367,0.86362,-0.44512,252.8
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.52663,0.49904,0.6882,202.05,0.81648,-0.071517,-0.57293,201.74,-0.2367,0.86362,-0.44512,252.18
> view matrix models
> #11,0.52663,0.49904,0.6882,206.71,0.81648,-0.071517,-0.57293,199.76,-0.2367,0.86362,-0.44512,250.25
> view matrix models
> #11,0.52663,0.49904,0.6882,206.58,0.81648,-0.071517,-0.57293,198.09,-0.2367,0.86362,-0.44512,255.9
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.27402,0.45257,0.84858,207.79,0.91259,0.15607,-0.37792,198.3,-0.30347,0.87797,-0.37024,256.3
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.27402,0.45257,0.84858,206.4,0.91259,0.15607,-0.37792,197.74,-0.30347,0.87797,-0.37024,253.54
> ui mousemode right select
> select clear
> select add #11
3748 atoms, 3849 bonds, 480 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.27402,0.45257,0.84858,204.56,0.91259,0.15607,-0.37792,198.64,-0.30347,0.87797,-0.37024,251.99
> select subtract #11
Nothing selected
> ui mousemode right "rotate selected models"
> select add #13
3 models selected
> view matrix models
> #13,0.99385,0.080221,0.076372,-27.987,-0.08412,0.99524,0.049272,9.0037,-0.072056,-0.055393,0.99586,25.956
> select subtract #13
Nothing selected
> undo
[Repeated 1 time(s)]
> select subtract #13
Nothing selected
> select add #11
3748 atoms, 3849 bonds, 480 residues, 1 model selected
> view matrix models
> #11,0.34539,0.61257,0.71096,203.58,0.92387,-0.088877,-0.37224,199.07,-0.16484,0.7854,-0.59664,250.97
> view matrix models
> #11,0.33564,0.58556,0.73788,203.76,0.91281,-0.008711,-0.40829,198.8,-0.23265,0.81058,-0.53743,251.3
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.33564,0.58556,0.73788,210.32,0.91281,-0.008711,-0.40829,192.61,-0.23265,0.81058,-0.53743,250.57
> view matrix models
> #11,0.33564,0.58556,0.73788,208.48,0.91281,-0.008711,-0.40829,187.9,-0.23265,0.81058,-0.53743,251.35
> view matrix models
> #11,0.33564,0.58556,0.73788,210.01,0.91281,-0.008711,-0.40829,187.91,-0.23265,0.81058,-0.53743,251.05
> select add #12
27061 atoms, 27388 bonds, 1 pseudobond, 2055 residues, 3 models selected
> select subtract #11
23313 atoms, 23539 bonds, 1 pseudobond, 1575 residues, 2 models selected
> select subtract #12
Nothing selected
> select add #11
3748 atoms, 3849 bonds, 480 residues, 1 model selected
> view matrix models
> #11,0.33564,0.58556,0.73788,210.72,0.91281,-0.008711,-0.40829,186.69,-0.23265,0.81058,-0.53743,253.36
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.42674,0.6292,0.64962,210.11,0.84806,-0.028892,-0.52911,186.35,-0.31415,0.77671,-0.54593,253.54
> view matrix models
> #11,0.43774,0.61225,0.65843,210.16,0.85392,-0.053884,-0.51761,186.43,-0.28143,0.78882,-0.5464,253.45
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.43774,0.61225,0.65843,210.26,0.85392,-0.053884,-0.51761,187.42,-0.28143,0.78882,-0.5464,253.55
> show #!3 models
> volume #3 level 0.08929
> select subtract #11
Nothing selected
> volume #3 level 0.1329
> hide #11 models
> show #11 models
> select add #11
3748 atoms, 3849 bonds, 480 residues, 1 model selected
> view matrix models
> #11,0.43774,0.61225,0.65843,209.39,0.85392,-0.053884,-0.51761,189.92,-0.28143,0.78882,-0.5464,254
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.21435,-0.44068,-0.8717,206.26,-0.91836,-0.21304,0.33352,197.02,-0.33268,0.87202,-0.35903,254.71
> view matrix models
> #11,-0.17968,-0.53738,-0.82398,206.56,-0.9824,0.054639,0.1786,196.04,-0.050954,0.84157,-0.53774,253.5
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.17968,-0.53738,-0.82398,201.93,-0.9824,0.054639,0.1786,209.1,-0.050954,0.84157,-0.53774,254.05
> view matrix models
> #11,-0.17968,-0.53738,-0.82398,197.13,-0.9824,0.054639,0.1786,210.39,-0.050954,0.84157,-0.53774,256.02
> hide #!3 models
> view matrix models
> #11,-0.17968,-0.53738,-0.82398,197.61,-0.9824,0.054639,0.1786,210.72,-0.050954,0.84157,-0.53774,255.89
> show #!3 models
> volume #3 level 0.1201
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.88371,-0.31387,0.34719,203.31,-0.15221,0.89422,0.42096,208.65,-0.44259,0.31916,-0.838,256.33
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.88371,-0.31387,0.34719,194.08,-0.15221,0.89422,0.42096,210.95,-0.44259,0.31916,-0.838,250.91
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.96557,-0.24904,0.075168,193.01,-0.196,0.88647,0.41923,211.04,-0.17104,0.39007,-0.90476,249.99
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.96557,-0.24904,0.075168,193.47,-0.196,0.88647,0.41923,212.64,-0.17104,0.39007,-0.90476,250.56
> volume #3 level 0.1201
> hide #!3 models
> view matrix models
> #11,-0.96557,-0.24904,0.075168,194.01,-0.196,0.88647,0.41923,216.6,-0.17104,0.39007,-0.90476,251.58
> view matrix models
> #11,-0.96557,-0.24904,0.075168,203.91,-0.196,0.88647,0.41923,218.46,-0.17104,0.39007,-0.90476,247.81
> view matrix models
> #11,-0.96557,-0.24904,0.075168,205.22,-0.196,0.88647,0.41923,218.39,-0.17104,0.39007,-0.90476,248.54
> show #!3 models
> hide #!3 models
> select subtract #11
Nothing selected
> hide #!13 models
> hide #!2 models
> select #11:346,352,366-368
43 atoms, 40 bonds, 5 residues, 1 model selected
> color sel byelement
> ui mousemode right select
> select clear
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/Serinc5_contacts_dock_run3_matches_density.png
> width 1749 height 1129 supersample 1 transparentBackground true
> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/CSSer5processing/Proceesing_Ninja/comparison_processing_2024_2025_withdocking_residues.cxs
> includeMaps true
——— End of log from Mon Nov 3 13:41:56 2025 ———
opened ChimeraX session
OpenGL version: 4.1 ATI-4.14.1
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 32 GB
System Firmware Version: 2075.120.2.0.0 (iBridge: 22.16.15072.0.0,0)
OS Loader Version: 577.140.2~30
Software:
System Software Overview:
System Version: macOS 13.7.6 (22H625)
Kernel Version: Darwin 22.6.0
Time since boot: 13 days, 8 hours, 22 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5500M:
Chipset Model: AMD Radeon Pro 5500M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0040
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32206U1-019
Option ROM Version: 113-D32206U1-019
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
LG HDR WQHD:
Resolution: 5120 x 2134
UI Looks like: 2560 x 1067 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: Thunderbolt/DisplayPort
Television: Yes
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.23.1
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.8
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
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
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
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