![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 days ago
Last modified 4 days ago
#20294 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sequence | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-26.3.1-arm64-arm-64bit
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Current thread 0x00000001f0467100 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 414 in event_loop
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1064 in init
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1229 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, PIL._imaging, chimerax.surface._surface, chimerax.map._map, openmm._openmm, openmm.app.internal.xtc_utils, openmm.app.internal.compiled, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, 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, chimerax.atom_search.ast, chimerax.chem_group._chem_group, kiwisolver._cext, chimerax.alignment_algs._sw, chimerax.alignment_algs._nw (total: 64)
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AttributeGraph Data 1024K 1
CG image 48K 3
ColorSync 4080K 255
CoreAnimation 2032K 115
CoreGraphics 112K 7
CoreUI image data 4096K 30
Foundation 48K 2
Kernel Alloc Once 32K 1
MALLOC 19.9G 1001
MALLOC guard page 4112K 4
MALLOC_LARGE (reserved) 248.8M 1 reserved VM address space (unallocated)
MALLOC_REALLOC (reserved) 3504K 1 reserved VM address space (unallocated)
Mach message 64K 3
OpenGL GLSL 256K 3
PROTECTED_MEMORY 16K 1
STACK GUARD 656K 41
Stack 201.9M 42
Stack Guard 56.0M 1
VM_ALLOCATE 455.8M 458
VM_ALLOCATE (reserved) 160.0M 2 reserved VM address space (unallocated)
__AUTH 5968K 657
__AUTH_CONST 90.5M 1043
__CTF 824 1
__DATA 43.9M 1177
__DATA_CONST 60.4M 1222
__DATA_DIRTY 8499K 900
__FONT_DATA 2352 1
__GLSLBUILTINS 5176K 1
__INFO_FILTER 8 1
__LINKEDIT 626.7M 175
__OBJC_RO 78.4M 1
__OBJC_RW 2571K 1
__TEXT 1.3G 1193
__TEXT (graphics) 232.6M 52
__TPRO_CONST 128K 2
dyld private memory 5840K 48
mapped file 680.7M 81
page table in kernel 11.9M 1
shared memory 3696K 25
=========== ======= =======
TOTAL 24.2G 8557
TOTAL, minus reserved VM space 23.8G 8557
",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "ba8eb564385daa0cd4243ce662f2bf4fe72b83e5",
"bug_type" : "309",
"roots_installed" : 0,
"trmStatus" : 1,
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "67648e5334a82511f4acf879",
"factorPackIds" : [
],
"deploymentId" : 240000008
},
{
"rolloutId" : "67d07cd6a7affa169ae21f45",
"factorPackIds" : [
],
"deploymentId" : 240000002
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/amy/Desktop/SPA
> AAT_HNE/3C11_Fab_AAT_NE/3c11_aat_hen_csparc.cxs"
Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300,
pixel 0.867, shown at level 0.0665, step 2, values float32
Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at
level 0.0841, step 1, values float32
Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size
300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32
Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size
180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32
Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867,
shown at level 0.0503, step 2, values float32
Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel
0.867, shown at level 0.0806, step 1, values float32
Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size
128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32
Opened cryosparc_P371_J937_003_volume_map.mrc as #14, grid size 300,300,300,
pixel 0.867, shown at level 0.0245, step 2, values float32
Opened cryosparc_P371_J937_003_volume_map.mrc z flip as #15, grid size
300,300,300, pixel 0.867, shown at level 0.0683, step 1, values float32
Opened cryosparc_P371_J948_003_volume_map.mrc as #21, grid size 300,300,300,
pixel 0.867, shown at level 0.0208, step 2, values float32
Opened cryosparc_P371_J948_003_volume_map.mrc z flip as #22, grid size
300,300,300, pixel 0.867, shown at level 0.0938, step 1, values float32
Opened J1122.mrc as #29, grid size 300,300,300, pixel 0.867, shown at level
0.071, step 2, values float32
Opened J1134.mrc as #34, grid size 300,300,300, pixel 0.867, shown at level
0.0707, step 2, values float32
Opened cryosparc_P483_molmap_of_combined_6A.mrc as #41, grid size 200,200,200,
pixel 1, shown at level 0.293, step 1, values float32
Opened AATHNEcombined map 6 as #8, grid size 43,51,63, pixel 2, shown at level
0.366, step 1, values float32
Opened copy of copy of AATHNEcombined map 6 as #45, grid size 43,51,63, pixel
2, shown at level 0.354, step 1, values float32
Log from Thu Mar 12 17:49:41 2026UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/amy/Desktop/SPA AAT_HNE/csparc.cxs"
Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300,
pixel 0.867, shown at level 0.0665, step 2, values float32
Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at
level 0.0841, step 1, values float32
Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size
300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32
Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size
180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32
Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867,
shown at level 0.0503, step 2, values float32
Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel
0.867, shown at level 0.0806, step 1, values float32
Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size
128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32
Opened cryosparc_P371_J937_003_volume_map.mrc as #14, grid size 300,300,300,
pixel 0.867, shown at level 0.0245, step 2, values float32
Opened cryosparc_P371_J937_003_volume_map.mrc z flip as #15, grid size
300,300,300, pixel 0.867, shown at level 0.0683, step 1, values float32
Opened cryosparc_P371_J948_003_volume_map.mrc as #21, grid size 300,300,300,
pixel 0.867, shown at level 0.0208, step 2, values float32
Opened cryosparc_P371_J948_003_volume_map.mrc z flip as #22, grid size
300,300,300, pixel 0.867, shown at level 0.0938, step 1, values float32
Opened J1122.mrc as #29, grid size 300,300,300, pixel 0.867, shown at level
0.071, step 2, values float32
Opened J1134.mrc as #34, grid size 300,300,300, pixel 0.867, shown at level
0.0707, step 2, values float32
Log from Wed Feb 11 13:24:40 2026UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/amy/Desktop/3C11_Fab_AAT_NE/csparc.cxs
Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300,
pixel 0.867, shown at level 0.0665, step 2, values float32
Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at
level 0.0841, step 1, values float32
Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size
300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32
Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size
180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32
Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867,
shown at level 0.0503, step 2, values float32
Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel
0.867, shown at level 0.0806, step 1, values float32
Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size
128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32
Opened cryosparc_P371_J937_003_volume_map.mrc as #14, grid size 300,300,300,
pixel 0.867, shown at level 0.0245, step 2, values float32
Opened cryosparc_P371_J937_003_volume_map.mrc z flip as #15, grid size
300,300,300, pixel 0.867, shown at level 0.0683, step 1, values float32
Opened cryosparc_P371_J948_003_volume_map.mrc as #21, grid size 300,300,300,
pixel 0.867, shown at level 0.0208, step 2, values float32
Opened cryosparc_P371_J948_003_volume_map.mrc z flip as #22, grid size
300,300,300, pixel 0.867, shown at level 0.0938, step 1, values float32
Opened J1122.mrc as #29, grid size 300,300,300, pixel 0.867, shown at level
0.071, step 2, values float32
Opened J1134.mrc as #34, grid size 300,300,300, pixel 0.867, shown at level
0.0707, step 2, values float32
Log from Sun Feb 1 23:24:08 2026UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/amy/Desktop/3C11_Fab_AAT_NE/csparc.cxs format session
Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300,
pixel 0.867, shown at level 0.0665, step 2, values float32
Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at
level 0.0841, step 1, values float32
Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size
300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32
Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size
180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32
Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867,
shown at level 0.0503, step 2, values float32
Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel
0.867, shown at level 0.0806, step 1, values float32
Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size
128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32
Opened cryosparc_P371_J937_003_volume_map.mrc as #14, grid size 300,300,300,
pixel 0.867, shown at level 0.0245, step 2, values float32
Opened cryosparc_P371_J937_003_volume_map.mrc z flip as #15, grid size
300,300,300, pixel 0.867, shown at level 0.0683, step 1, values float32
Opened cryosparc_P371_J948_003_volume_map.mrc as #21, grid size 300,300,300,
pixel 0.867, shown at level 0.0208, step 2, values float32
Opened cryosparc_P371_J948_003_volume_map.mrc z flip as #22, grid size
300,300,300, pixel 0.867, shown at level 0.0938, step 1, values float32
Opened J1122.mrc as #29, grid size 300,300,300, pixel 0.867, shown at level
0.071, step 2, values float32
Opened J1134.mrc as #34, grid size 300,300,300, pixel 0.867, shown at level
0.0707, step 2, values float32
Log from Tue Jan 6 13:31:49 2026UCSF ChimeraX version: 1.9rc202411230619
(2024-11-23)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/apple/Downloads/csparc.cxs
Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300,
pixel 0.867, shown at level 0.0665, step 2, values float32
Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at
level 0.0841, step 1, values float32
Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size
300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32
Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size
180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32
Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867,
shown at level 0.0503, step 2, values float32
Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel
0.867, shown at level 0.0806, step 1, values float32
Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size
128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32
Opened cryosparc_P371_J937_003_volume_map.mrc as #14, grid size 300,300,300,
pixel 0.867, shown at level 0.0245, step 2, values float32
Opened cryosparc_P371_J937_003_volume_map.mrc z flip as #15, grid size
300,300,300, pixel 0.867, shown at level 0.0683, step 1, values float32
Opened cryosparc_P371_J948_003_volume_map.mrc as #21, grid size 300,300,300,
pixel 0.867, shown at level 0.0208, step 2, values float32
Opened cryosparc_P371_J948_003_volume_map.mrc z flip as #22, grid size
300,300,300, pixel 0.867, shown at level 0.0938, step 1, values float32
Log from Wed Dec 31 02:28:23 2025UCSF ChimeraX version: 1.9rc202411230619
(2024-11-23)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/apple/Downloads/csparc.cxs
Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300,
pixel 0.867, shown at level 0.0665, step 2, values float32
Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at
level 0.0841, step 1, values float32
Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size
300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32
Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size
180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32
Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867,
shown at level 0.0503, step 2, values float32
Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel
0.867, shown at level 0.0806, step 1, values float32
Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size
128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32
Opened cryosparc_P371_J937_003_volume_map.mrc as #14, grid size 300,300,300,
pixel 0.867, shown at level 0.0245, step 2, values float32
Opened cryosparc_P371_J937_003_volume_map.mrc z flip as #15, grid size
300,300,300, pixel 0.867, shown at level 0.0683, step 1, values float32
Opened cryosparc_P371_J948_003_volume_map.mrc as #21, grid size 300,300,300,
pixel 0.867, shown at level 0.0208, step 2, values float32
Opened cryosparc_P371_J948_003_volume_map.mrc z flip as #22, grid size
300,300,300, pixel 0.867, shown at level 0.0938, step 1, values float32
Log from Wed Dec 10 00:50:43 2025UCSF ChimeraX version: 1.9rc202411230619
(2024-11-23)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/apple/Downloads/csparc.cxs
Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300,
pixel 0.867, shown at level 0.0665, step 2, values float32
Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at
level 0.0841, step 1, values float32
Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size
300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32
Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size
180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32
Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867,
shown at level 0.0503, step 2, values float32
Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel
0.867, shown at level 0.0806, step 1, values float32
Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size
128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32
Log from Fri Nov 28 18:17:17 2025UCSF ChimeraX version: 1.9rc202411230619
(2024-11-23)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/apple/Downloads/csparc.cxs
Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300,
pixel 0.867, shown at level 0.0665, step 2, values float32
Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at
level 0.0841, step 1, values float32
Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size
300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32
Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size
180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32
Log from Tue Nov 25 15:20:48 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9rc202411230619 (2024-11-23)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 1ezx format mmcif fromDatabase pdb
1ezx title:
Crystal structure of A serpin:protease complex [more info...]
Chain information for 1ezx #1
---
Chain | Description | UniProt
A | ALPHA-1-ANTITRYPSIN | A1AT_HUMAN 24-358
B | ALPHA-1-ANTITRYPSIN | A1AT_HUMAN 359-394
C | TRYPSIN | TRY1_BOVIN 42-245
> open /Users/apple/Downloads/cryosparc_P371_J880_003_volume_map.mrc
Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300,
pixel 0.867, shown at level 0.0177, step 2, values float32
> volume #2 level 0.06652
> ui mousemode right "translate selected models"
> select add #1
3984 atoms, 3982 bonds, 5 pseudobonds, 592 residues, 3 models selected
> view matrix models #1,1,0,0,22.115,0,1,0,63.09,0,0,1,71.823
> view matrix models #1,1,0,0,69.177,0,1,0,79.741,0,0,1,64.119
> view matrix models #1,1,0,0,67.012,0,1,0,77.327,0,0,1,54.335
> view matrix models #1,1,0,0,68.613,0,1,0,71.318,0,0,1,51.449
> ui tool show "Fit in Map"
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 3984 atoms
average map value = 0.0438, steps = 92
shifted from previous position = 3.55
rotated from previous position = 4.42 degrees
atoms outside contour = 2880, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.99872483 -0.00989522 0.04950557 63.11308004
0.00699761 0.99827076 0.05836545 67.58136236
-0.04999751 -0.05794461 0.99706703 56.37622316
Axis -0.75528783 0.64614759 0.10969770
Axis point 0.00000000 1024.64866555 -1103.37084637
Rotation angle (degrees) 4.41598404
Shift along axis 2.18333524
> view matrix models
> #1,0.99872,-0.0098952,0.049506,62.468,0.0069976,0.99827,0.058365,78.039,-0.049998,-0.057945,0.99707,58.786
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.95028,-0.27274,-0.15028,221.56,0.30912,-0.88449,-0.34946,175.7,-0.037612,-0.37854,0.92482,78.268
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 3984 atoms
average map value = 0.04798, steps = 140
shifted from previous position = 7.9
rotated from previous position = 12.7 degrees
atoms outside contour = 2817, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
-0.90965137 -0.21420693 -0.35587888 224.37202412
0.34819532 -0.86039384 -0.37213231 169.35532345
-0.22648268 -0.46242602 0.85724429 105.26930309
Axis -0.15458157 -0.22152447 0.96282472
Axis point 107.00674340 114.53127832 0.00000000
Rotation angle (degrees) 163.01876555
Shift along axis 29.15575838
> view matrix models
> #1,-0.93537,-0.33888,0.10125,206.37,0.28885,-0.89713,-0.33425,173.15,0.2041,-0.2834,0.93703,61.97
> remove /C
Unknown command: remove /C
> delete /C
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 2975 atoms
average map value = 0.05683, steps = 168
shifted from previous position = 10.2
rotated from previous position = 20.9 degrees
atoms outside contour = 1876, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
-0.98775248 -0.03216686 0.15267718 185.97005837
0.01404291 -0.99287467 -0.11833294 193.09005228
0.15539570 -0.11473962 0.98116614 52.60294093
Axis 0.07739391 -0.05855237 0.99527976
Axis point 89.79478279 99.15188295 0.00000000
Rotation angle (degrees) 178.66978984
Shift along axis 55.44171271
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 2975 atoms
average map value = 0.05683, steps = 44
shifted from previous position = 0.00306
rotated from previous position = 0.00868 degrees
atoms outside contour = 1876, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
-0.98775300 -0.03230499 0.15264466 185.98147456
0.01419042 -0.99287622 -0.11830233 193.08167122
0.15537901 -0.11468739 0.98117489 52.59959002
Axis 0.07738151 -0.05853153 0.99528195
Axis point 89.79393478 99.15365724 0.00000000
Rotation angle (degrees) 178.66156873
Shift along axis 55.44158488
> view matrix models
> #1,-0.34306,0.064653,-0.93709,202.25,-0.15112,-0.98843,-0.012871,197.23,-0.92708,0.1372,0.34886,143.06
> view matrix models
> #1,0.89084,0.24868,-0.38022,79.922,0.1402,-0.94652,-0.29059,192.22,-0.43215,0.20556,-0.87806,178.59
> view matrix models
> #1,0.98069,0.15076,0.12459,50.828,0.17789,-0.95233,-0.24786,187.69,0.081282,0.26523,-0.96075,146.99
> transparency #2 50
> view matrix models
> #1,0.29239,0.037619,0.95556,53.368,0.22932,-0.97283,-0.03187,173.11,0.9284,0.22844,-0.29308,56.382
> view matrix models
> #1,-0.29179,0.14333,0.94568,84.773,0.13863,-0.97193,0.19008,165.94,0.94638,0.18656,0.26373,25.435
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 2975 atoms
average map value = 0.05731, steps = 92
shifted from previous position = 3.83
rotated from previous position = 8.94 degrees
atoms outside contour = 1851, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
-0.32142151 0.28922900 0.90168442 78.62508488
0.10483022 -0.93549119 0.33744164 157.26649378
0.94111574 0.20298478 0.27036706 21.13366302
Axis -0.58056816 -0.17025957 -0.79621121
Axis point 36.79057462 75.39561878 -0.00000000
Rotation angle (degrees) 173.35036530
Shift along axis -89.25020548
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 2975 atoms
average map value = 0.05731, steps = 76
shifted from previous position = 0.0143
rotated from previous position = 0.0108 degrees
atoms outside contour = 1850, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
-0.32139468 0.28930309 0.90167022 78.61286146
0.10496741 -0.93543603 0.33755190 157.24594170
0.94110961 0.20313337 0.27027676 21.11828838
Axis -0.58058094 -0.17034675 -0.79618324
Axis point 36.78722862 75.38632197 0.00000000
Rotation angle (degrees) 173.35241654
Shift along axis -89.24149146
> view matrix models
> #1,0.48423,0.47971,0.73171,25.463,0.23276,-0.87679,0.42079,140.68,0.84341,-0.033442,-0.53622,88.647
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 2975 atoms
average map value = 0.05854, steps = 96
shifted from previous position = 2.57
rotated from previous position = 9.29 degrees
atoms outside contour = 1796, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.39156198 0.46621567 0.79329828 28.63896931
0.32834063 -0.87617582 0.35285743 137.96501568
0.85957643 0.12230650 -0.49615469 78.33453532
Axis -0.83325343 -0.23954143 -0.49830575
Axis point 0.00000000 66.13906102 25.80824474
Rotation angle (degrees) 172.04797842
Shift along axis -95.94640636
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 2975 atoms
average map value = 0.05854, steps = 72
shifted from previous position = 0.00208
rotated from previous position = 0.0113 degrees
atoms outside contour = 1796, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.39171342 0.46612484 0.79327690 28.63726861
0.32836586 -0.87622221 0.35271873 137.97292978
0.85949779 0.12232039 -0.49628748 78.34647546
Axis -0.83330036 -0.23950649 -0.49824406
Axis point 0.00000000 66.14388335 25.81952433
Rotation angle (degrees) 172.05372561
Shift along axis -95.94452502
> view matrix models
> #1,0.76487,0.62103,0.17117,31.524,0.60943,-0.78369,0.12011,127.91,0.20873,0.012451,-0.97789,154.56
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 2975 atoms
average map value = 0.05756, steps = 152
shifted from previous position = 4.36
rotated from previous position = 22.9 degrees
atoms outside contour = 1854, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.91851505 0.27415782 0.28489928 35.47934780
0.28051968 -0.95965858 0.01908170 161.02943922
0.27863743 0.06239303 -0.95836751 146.25557472
Axis 0.97941439 0.14160128 0.14386290
Axis point 0.00000000 77.18823065 71.36819300
Rotation angle (degrees) 178.73303939
Shift along axis 78.59170916
> view matrix models
> #1,0.70928,0.23412,0.66491,29.192,0.22662,-0.9689,0.099416,160.36,0.6675,0.080168,-0.74028,107.68
> view matrix models
> #1,0.38932,0.16756,0.90573,39.677,0.11688,-0.98435,0.13187,166.42,0.91366,0.054523,-0.40281,73.929
> view matrix models
> #1,0.33533,0.23749,0.91168,38.512,0.22246,-0.9603,0.16833,156.1,0.91546,0.14637,-0.37485,66.587
> view matrix models
> #1,0.33533,0.23749,0.91168,38.861,0.22246,-0.9603,0.16833,151.64,0.91546,0.14637,-0.37485,67.054
> view matrix models
> #1,0.34573,0.097318,0.93327,45.492,0.021529,-0.99517,0.095797,170.8,0.93809,-0.013027,-0.34615,73.665
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 2975 atoms
average map value = 0.05854, steps = 136
shifted from previous position = 9.44
rotated from previous position = 25.1 degrees
atoms outside contour = 1797, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.39128073 0.46623746 0.79342424 28.64047706
0.32828593 -0.87615611 0.35295725 137.95838588
0.85972538 0.12236464 -0.49588220 78.32133865
Axis -0.83316813 -0.23955669 -0.49844103
Axis point 0.00000000 66.13417831 25.79650241
Rotation angle (degrees) 172.04571172
Shift along axis -95.94975542
> view matrix models
> #1,0.39128,0.46624,0.79342,25.073,0.32829,-0.87616,0.35296,137.6,0.85973,0.12236,-0.49588,78.077
> view matrix models
> #1,-0.056102,0.1979,0.97862,59.23,0.073542,-0.97668,0.20173,168.77,0.99571,0.083287,0.04024,40.63
> view matrix models
> #1,-0.064697,0.19676,0.97831,59.866,-0.033318,-0.98025,0.19495,176.2,0.99735,-0.019983,0.069975,45.097
> view matrix models
> #1,-0.064697,0.19676,0.97831,60.856,-0.033318,-0.98025,0.19495,173.38,0.99735,-0.019983,0.069975,44.14
> view matrix models
> #1,-0.064697,0.19676,0.97831,62.425,-0.033318,-0.98025,0.19495,171.85,0.99735,-0.019983,0.069975,46.927
> view matrix models
> #1,0.048374,0.23427,0.97097,53.348,-0.027021,-0.97144,0.23574,168.54,0.99846,-0.037639,-0.040662,54.362
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 2975 atoms
average map value = 0.05548, steps = 116
shifted from previous position = 2.18
rotated from previous position = 10.2 degrees
atoms outside contour = 1897, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.15476290 0.36480201 0.91813285 40.06056626
0.00453943 -0.92958252 0.36858613 155.48377322
0.98794121 -0.05287566 -0.14552088 61.55028255
Axis -0.75418435 -0.12491849 -0.64467149
Axis point 0.00000000 74.79947560 0.01397902
Rotation angle (degrees) 163.77466905
Shift along axis -89.31556288
> view matrix models
> #1,0.15476,0.3648,0.91813,43.614,0.0045394,-0.92958,0.36859,155.22,0.98794,-0.052876,-0.14552,59.521
> view matrix models
> #1,-0.2078,0.33394,0.9194,68.56,-0.052237,-0.94237,0.33048,161.84,0.97677,0.020648,0.21327,34.9
> view matrix models
> #1,-0.21574,0.16972,0.96159,76.632,-0.13117,-0.98089,0.1437,180.08,0.9676,-0.095125,0.23388,41.35
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 2975 atoms
average map value = 0.05783, steps = 140
shifted from previous position = 8.76
rotated from previous position = 14.8 degrees
atoms outside contour = 1859, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
-0.45352763 0.10818223 0.88465208 99.24914335
-0.11633057 -0.99129935 0.06158562 193.39501529
0.88361750 -0.07498130 0.46216655 30.32738546
Axis -0.51968455 0.00393692 -0.85434915
Axis point 47.88058461 94.47454852 0.00000000
Rotation angle (degrees) 172.44984306
Shift along axis -76.72704192
> view matrix models
> #1,-0.44996,0.138,0.88232,97.338,-0.1451,-0.98616,0.080249,193.83,0.88118,-0.091912,0.46376,31.423
> view matrix models
> #1,-0.44996,0.138,0.88232,96.943,-0.1451,-0.98616,0.080249,180.07,0.88118,-0.091912,0.46376,31.456
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 2975 atoms
average map value = 0.05816, steps = 144
shifted from previous position = 5.29
rotated from previous position = 25.5 degrees
atoms outside contour = 1860, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
-0.76791109 0.07342342 0.63633447 137.05037337
0.02287887 -0.98963117 0.14179815 171.02871657
0.64014773 0.12344698 0.75826890 16.52925526
Axis -0.34041716 -0.07073658 -0.93760999
Axis point 66.71618726 84.08739228 0.00000000
Rotation angle (degrees) 178.45546636
Shift along axis -74.25028018
> volume flip #2 axis z
Opened cryosparc_P371_J880_003_volume_map.mrc z flip as #3, grid size
300,300,300, pixel 0.867, shown at step 1, values float32
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 2975 atoms
average map value = 0.05816, steps = 44
shifted from previous position = 0.00304
rotated from previous position = 0.0131 degrees
atoms outside contour = 1859, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
-0.76779231 0.07330789 0.63649111 137.03880955
0.02299050 -0.98964048 0.14171507 171.02535003
0.64028619 0.12344099 0.75815296 16.52599590
Axis -0.34050650 -0.07071503 -0.93757917
Axis point 66.70481841 84.08969330 0.00000000
Rotation angle (degrees) 178.46235923
Shift along axis -74.25109879
> view matrix models
> #1,-0.52389,0.12388,0.84273,106.41,0.091727,-0.97541,0.20041,162.36,0.84683,0.18229,0.49964,14.777
> select add #3
2975 atoms, 2968 bonds, 437 residues, 3 models selected
> select subtract #3
2975 atoms, 2968 bonds, 437 residues, 1 model selected
> view matrix models
> #1,-0.52389,0.12388,0.84273,105.24,0.091727,-0.97541,0.20041,169.49,0.84683,0.18229,0.49964,54.589
> view matrix models
> #1,-0.52389,0.12388,0.84273,103,0.091727,-0.97541,0.20041,168.04,0.84683,0.18229,0.49964,53.744
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 2975 atoms
average map value = 0.05198, steps = 396
shifted from previous position = 26.6
rotated from previous position = 41.8 degrees
atoms outside contour = 2024, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
-0.40282969 0.31103532 0.86080501 84.94134983
0.59685966 -0.62373813 0.50468732 103.56065454
0.69389249 0.71708282 0.06561581 32.32204409
Axis 0.54006522 0.42441412 0.72677522
Axis point 26.67261820 43.96459459 0.00000000
Rotation angle (degrees) 168.65952926
Shift along axis 113.31733317
> view matrix models
> #1,-0.43926,0.065153,0.89599,100.22,0.59516,-0.72598,0.34457,119.21,0.67293,0.68462,0.28012,23.176
> view matrix models
> #1,-0.43926,0.065153,0.89599,90.909,0.59516,-0.72598,0.34457,101.79,0.67293,0.68462,0.28012,39.972
> view matrix models
> #1,-0.86466,-0.41381,0.28483,182.78,0.49939,-0.76955,0.39798,107.46,0.054503,0.48636,0.87206,57.135
> view matrix models
> #1,-0.41714,-0.50359,-0.75657,220.21,0.34751,-0.85757,0.37922,123.61,-0.83978,-0.10473,0.53273,169.98
> view matrix models
> #1,0.75417,0.076431,-0.65222,104.02,0.19721,-0.97372,0.11393,155.7,-0.62637,-0.21455,-0.74942,237.56
> view matrix models
> #1,0.59893,0.091914,-0.79551,121.31,0.19286,-0.98071,0.031893,161.17,-0.77723,-0.17253,-0.6051,236.24
> view matrix models
> #1,0.59893,0.091914,-0.79551,120.05,0.19286,-0.98071,0.031893,163.86,-0.77723,-0.17253,-0.6051,238.3
> view matrix models
> #1,0.60587,0.10394,-0.78874,118.48,0.22025,-0.97459,0.040753,161.22,-0.76446,-0.19841,-0.61337,239.55
> view matrix models
> #1,0.60587,0.10394,-0.78874,137.03,0.22025,-0.97459,0.040753,164.86,-0.76446,-0.19841,-0.61337,244.11
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 2975 atoms
average map value = 0.05241, steps = 240
shifted from previous position = 27.2
rotated from previous position = 10.6 degrees
atoms outside contour = 2020, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.57403834 -0.00393553 -0.81881897 142.71357757
0.04701479 -0.99818033 0.03775763 187.83819388
-0.81747758 -0.06017093 -0.57280875 212.09998405
Axis -0.88704943 -0.01215043 0.46151455
Axis point 0.00000000 96.46648529 140.25698861
Rotation angle (degrees) 176.83571969
Shift along axis -30.98908429
> view matrix models
> #1,0.50366,0.028512,-0.86343,147.82,0.16923,-0.98335,0.066244,177.48,-0.84716,-0.17948,-0.5001,217.05
> view matrix models
> #1,0.50366,0.028512,-0.86343,159.38,0.16923,-0.98335,0.066244,163.53,-0.84716,-0.17948,-0.5001,218.36
> view matrix models
> #1,0.77888,-0.021397,-0.6268,131.11,0.011385,-0.99877,0.048242,175.59,-0.62706,-0.044711,-0.77768,212.22
> view matrix models
> #1,0.80541,-0.036391,-0.5916,128.29,-0.023432,-0.99929,0.029569,178.93,-0.59225,-0.0099531,-0.80569,209.51
> view matrix models
> #1,0.80541,-0.036391,-0.5916,124.59,-0.023432,-0.99929,0.029569,182.08,-0.59225,-0.0099531,-0.80569,208.91
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 2975 atoms
average map value = 0.06114, steps = 180
shifted from previous position = 15
rotated from previous position = 14.2 degrees
atoms outside contour = 1746, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.85347860 0.03851228 -0.51970287 104.90951223
-0.07623353 -0.97731057 -0.19761705 201.13931543
-0.51552180 0.20828070 -0.83117774 180.17182734
Axis 0.96224006 -0.00991186 -0.27202175
Axis point 0.00000000 90.37179533 116.08940430
Rotation angle (degrees) 167.82414204
Shift along axis 49.94381521
> view matrix models
> #1,0.85348,0.038512,-0.5197,94.645,-0.076234,-0.97731,-0.19762,192.73,-0.51552,0.20828,-0.83118,215.52
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 2975 atoms
average map value = 0.04998, steps = 228
shifted from previous position = 24.7
rotated from previous position = 22.8 degrees
atoms outside contour = 2007, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.83373907 0.05761081 -0.54914494 106.68752994
-0.27258804 -0.82195371 -0.50008786 229.20333513
-0.48018219 0.56663312 -0.66959090 165.21182517
Axis 0.95346344 -0.06164073 -0.29514047
Axis point 0.00000000 89.71271679 136.26536856
Rotation angle (degrees) 145.98619039
Shift along axis 38.83370161
> view matrix models
> #1,0.85957,-0.051768,-0.50839,109.34,-0.30914,-0.84485,-0.43665,229.25,-0.40691,0.5325,-0.74221,166.84
> view matrix models
> #1,0.85957,-0.051768,-0.50839,105.72,-0.30914,-0.84485,-0.43665,214.62,-0.40691,0.5325,-0.74221,185.48
> view matrix models
> #1,0.90687,0.19702,-0.37252,79.626,0.12723,-0.97073,-0.20369,180.91,-0.40175,0.13732,-0.90539,218.74
> view matrix models
> #1,0.67914,0.18357,0.71068,32.037,0.24568,-0.96923,0.015585,160.52,0.69167,0.16401,-0.70334,135.59
> view matrix models
> #1,0.17493,0.05579,0.983,56.185,0.11322,-0.99291,0.036205,169.22,0.97805,0.10496,-0.18,90.508
> view matrix models
> #1,0.77968,0.065182,0.62277,37.951,0.11391,-0.99274,-0.038712,173.52,0.61572,0.10113,-0.78145,148.81
> view matrix models
> #1,0.92537,0.30742,-0.22176,62.951,0.27327,-0.94648,-0.17175,168.25,-0.26269,0.09833,-0.95986,215.41
> view matrix models
> #1,0.70434,0.40439,-0.58342,92.157,0.29038,-0.9141,-0.28304,171.65,-0.64776,0.02994,-0.76126,232.61
> view matrix models
> #1,0.63232,0.36591,-0.68285,104.88,0.25844,-0.93057,-0.25933,173.32,-0.73033,-0.012492,-0.68298,235.92
> view matrix models
> #1,0.63232,0.36591,-0.68285,105.28,0.25844,-0.93057,-0.25933,173.87,-0.73033,-0.012492,-0.68298,234.43
> view matrix models
> #1,0.62644,0.35038,-0.69628,107.38,0.25038,-0.93639,-0.24594,173.97,-0.73816,-0.020267,-0.67432,234.9
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 2975 atoms
average map value = 0.04135, steps = 172
shifted from previous position = 17.5
rotated from previous position = 15.7 degrees
atoms outside contour = 2209, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.64106806 0.54805599 -0.53727682 84.29416786
0.45670740 -0.83502441 -0.30684294 171.83349628
-0.61680637 -0.04867109 -0.78560870 224.33733641
Axis 0.90532451 0.27888420 -0.32032972
Axis point 0.00000000 63.39099370 133.30398496
Rotation angle (degrees) 171.80252826
Shift along axis 52.37330856
> volume #3 level 0.08411
> view matrix models
> #1,0.89403,0.11377,0.43333,38.242,0.12475,-0.99218,0.0031177,184.59,0.43029,0.051272,-0.90123,158.14
> view matrix models
> #1,-0.18632,0.03739,0.98178,79.976,-0.079477,-0.99657,0.02287,196.75,0.97927,-0.073767,0.18865,67.401
> view matrix models
> #1,-0.90953,0.27518,-0.3115,186.77,-0.18965,-0.94164,-0.2781,217.91,-0.36985,-0.19387,0.90864,118.99
> view matrix models
> #1,0.24398,0.16972,-0.95481,156.97,0.38319,-0.92132,-0.065848,167.79,-0.89086,-0.34981,-0.28982,231.39
> view matrix models
> #1,0.42166,0.25626,-0.86979,135.42,0.41641,-0.90683,-0.065311,164.75,-0.80549,-0.33465,-0.48908,236.59
> view matrix models
> #1,0.47933,0.24843,-0.84174,130.58,0.4184,-0.90778,-0.029658,162.61,-0.77148,-0.33797,-0.53907,237.53
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.47933,0.24843,-0.84174,128.8,0.4184,-0.90778,-0.029658,153.85,-0.77148,-0.33797,-0.53907,247.51
> fitmap #1 inMap #3
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc z flip
(#3) using 2975 atoms
average map value = 0.05446, steps = 68
shifted from previous position = 3.18
rotated from previous position = 7.84 degrees
atoms outside contour = 2178, contour level = 0.08411
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc z
flip (#3) coordinates:
Matrix rotation and translation
0.52841759 0.14565472 -0.83639676 133.99651702
0.41790523 -0.90217777 0.10691341 147.19357847
-0.73900613 -0.40602951 -0.53759648 249.57659595
Axis -0.87112860 -0.16539807 0.46236180
Axis point 0.00000000 83.46704951 147.99690601
Rotation angle (degrees) 162.87766715
Shift along axis -25.67904816
> view matrix models
> #1,0.228,0.04128,-0.97279,167.46,0.36006,-0.93185,0.04485,156.3,-0.90464,-0.36049,-0.22733,239.34
> view matrix models
> #1,0.228,0.04128,-0.97279,168.72,0.36006,-0.93185,0.04485,153.1,-0.90464,-0.36049,-0.22733,238.66
> fitmap #1 inMap #3
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc z flip
(#3) using 2975 atoms
average map value = 0.08066, steps = 176
shifted from previous position = 5.39
rotated from previous position = 39.4 degrees
atoms outside contour = 1661, contour level = 0.08411
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc z
flip (#3) coordinates:
Matrix rotation and translation
-0.38244590 0.10991711 -0.91741668 203.00581119
0.07750617 -0.98558322 -0.15039445 183.86146589
-0.92072141 -0.12862319 0.36841301 193.39522834
Axis 0.55561740 0.08433916 -0.82714945
Axis point 167.56182272 100.48395710 0.00000000
Rotation angle (degrees) 178.87739199
Shift along axis -31.66647401
> save /Users/apple/Downloads/csparc.cxs includeMaps true
> select subtract #1
Nothing selected
> select add #3
2 models selected
> save /Users/apple/Downloads/flipped_J880.mrc models #3
> open /Users/apple/Downloads/3C11_Fab_D_1292144377_model-annotate_P1_HL-
> coot-0.pdb /Users/apple/Downloads/1ezx_moved-coot-0.pdb
Summary of feedback from opening
/Users/apple/Downloads/3C11_Fab_D_1292144377_model-annotate_P1_HL-coot-0.pdb
---
warnings | Start residue of secondary structure not found: HELIX 8 AA8 THR I 28 TYR I 32 5 5
Start residue of secondary structure not found: HELIX 9 AA9 ASN I 73 LYS I 75
5 3
Start residue of secondary structure not found: HELIX 10 AB1 LYS I 83 THR I 87
5 5
Start residue of secondary structure not found: HELIX 11 AB2 SER I 156 SER I
158 5 3
Start residue of secondary structure not found: HELIX 12 AB3 PRO I 200 SER I
203 5 4
49 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (22 )
Cannot find LINK/SSBOND residue CYS (128 )
Cannot find LINK/SSBOND residue CYS (140 )
Cannot find LINK/SSBOND residue CYS (24 )
Cannot find LINK/SSBOND residue CYS (135 )
3C11_Fab_D_1292144377_model-annotate_P1_HL-coot-0.pdb title:
Fab fragment of an antibody that recognises all conformations of
α-1-antitrypsin [more info...]
Chain information for 3C11_Fab_D_1292144377_model-annotate_P1_HL-coot-0.pdb #4
---
Chain | Description
H | fab 3C11 heavy chain
L | fab 3C11 light chain
128 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Chain information for 1ezx_moved-coot-0.pdb #5
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> save /Users/apple/Downloads/csparc.cxs includeMaps true
> open /Users/apple/Downloads/3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb
Summary of feedback from opening
/Users/apple/Downloads/3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb
---
warnings | Start residue of secondary structure not found: HELIX 8 AA8 THR I 28 TYR I 32 5 5
Start residue of secondary structure not found: HELIX 9 AA9 ASN I 73 LYS I 75
5 3
Start residue of secondary structure not found: HELIX 10 AB1 LYS I 83 THR I 87
5 5
Start residue of secondary structure not found: HELIX 11 AB2 SER I 156 SER I
158 5 3
Start residue of secondary structure not found: HELIX 12 AB3 PRO I 200 SER I
203 5 4
49 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (22 )
Cannot find LINK/SSBOND residue CYS (128 )
Cannot find LINK/SSBOND residue CYS (140 )
Cannot find LINK/SSBOND residue CYS (24 )
Cannot find LINK/SSBOND residue CYS (135 )
3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb title:
Fab fragment of an antibody that recognises all conformations of
α-1-antitrypsin [more info...]
Chain information for 3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb #6
---
Chain | Description
H | fab 3C11 heavy chain
L | fab 3C11 light chain
128 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> mmaker #6 to #4
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3C11_Fab_D_1292144377_model-annotate_P1_HL-coot-0.pdb, chain L (#4)
with 3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb, chain L (#6), sequence
alignment score = 1108.5
RMSD between 208 pruned atom pairs is 0.000 angstroms; (across all 208 pairs:
0.000)
> hide #!4 models
> save /Users/apple/Downloads/csparc.cxs includeMaps true
> open /Users/apple/Downloads/cryosparc_P371_J891_003_volume_map.mrc
Opened cryosparc_P371_J891_003_volume_map.mrc as #7, grid size 300,300,300,
pixel 0.867, shown at level 0.0162, step 2, values float32
> volume #7 level 0.0734
> select subtract #3
Nothing selected
> hide #5 models
> hide #!6 models
> volume #7 level 0.05238
> hide #!7 models
> show #!6 models
> show #5 models
> show #!3 models
> show #!7 models
> hide #!7 models
> open "/Users/apple/Downloads/cryosparc_P371_J882_005_volume_map (1).mrc"
Opened cryosparc_P371_J882_005_volume_map (1).mrc as #8, grid size
300,300,300, pixel 0.867, shown at level 0.0235, step 2, values float32
> hide #5 models
> hide #!6 models
> volume #8 level 0.0555
> volume flip #8 axis z
Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size
300,300,300, pixel 0.867, shown at step 1, values float32
> volume #9 level 0.06023
> show #!1 models
> hide #!1 models
> show #5 models
> hide #5 models
> volume copy #5
> show #5 models
> hide #5 models
> show #!1 models
> transparency #8 50
> transparency #9 50
> show #!4 models
> hide #!4 models
> show #!6 models
> close #8
> show #!7 models
> hide #!7 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> open /Users/apple/Downloads/cryosparc_P371_J881_class_08_00006_volume.mrc
Opened cryosparc_P371_J881_class_08_00006_volume.mrc as #8, grid size
180,180,180, pixel 1.44, shown at level 0.0542, step 1, values float32
> volume #8 level 0.122
> volume flip #8 axis z
Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size
180,180,180, pixel 1.44, shown at step 1, values float32
> select down
Nothing selected
> select down
Nothing selected
> transparency #8 50
> transparency #10 50
> hide #!10 models
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> close #8
> show #!7 models
> hide #!7 models
> close #7
> save /Users/apple/Downloads/csparc.cxs includeMaps true
——— End of log from Tue Nov 25 15:20:48 2025 ———
opened ChimeraX session
> show #!3 models
> open 5A0C fromDatabase pdb format mmcif
5a0c title:
Crystal Structure of human neutrophil elastase in complex with a
dihydropyrimidone inhibitor [more info...]
Chain information for 5a0c #7
---
Chain | Description | UniProt
A B | NEUTROPHIL ELASTASE | ELNE_HUMAN 16-252
Non-standard residues in 5a0c #7
---
FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose;
L-fucose; fucose)
JJV — (6S)-6-(4-cyano-2-methylsulfonyl-
phenyl)-4-methyl-2-oxidanylidene-3-[3-(trifluoromethyl)phenyl]-1,6-dihydropyrimidine-5-carbonitrile
MES — 2-(N-morpholino)-ethanesulfonic acid
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
XPE — 3,6,9,12,15,18,21,24,27-nonaoxanonacosane-1,29-diol (decaethylene
glycol)
5a0c mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> hide #!1 models
> show #!1 models
> open 1ezx fromDatabase pdb format mmcif
1ezx title:
Crystal structure of A serpin:protease complex [more info...]
Chain information for 1ezx #8
---
Chain | Description | UniProt
A | ALPHA-1-ANTITRYPSIN | A1AT_HUMAN 24-358
B | ALPHA-1-ANTITRYPSIN | A1AT_HUMAN 359-394
C | TRYPSIN | TRY1_BOVIN 42-245
> select #8/A
2686 atoms, 2674 bonds, 398 residues, 1 model selected
> mmaker #8 to #1
Computing secondary structure
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 1ezx, chain A (#1) with 1ezx, chain A (#8), sequence alignment
score = 1734
RMSD between 335 pruned atom pairs is 0.000 angstroms; (across all 335 pairs:
0.000)
> select #7/B, C, D, E, F
1965 atoms, 1848 bonds, 391 residues, 1 model selected
> delete #7/B, C, D, E, F
> mmaker #7 to #8
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1ezx, chain C (#8) with 5a0c, chain A (#7), sequence alignment
score = 241.2
RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
3.073)
> hide #7#!1,6,8 atoms
> save /Users/apple/Downloads/csparc.cxs includeMaps true
> open /Users/apple/Downloads/cryosparc_P371_J916_map.mrc
Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867,
shown at level 0.0238, step 2, values float32
> volume flip #11 axis z
Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel
0.867, shown at step 1, values float32
> volume #12 level 0.06229
> transparency #12 50
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!6 models
> show #!6 models
> hide #!8 models
> show #!8 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #7 models
> show #7 models
> hide #!8 models
> ui tool show "Fit in Map"
> fitmap #7 inMap #12
Fit molecule 5a0c (#7) to map cryosparc_P371_J916_map.mrc z flip (#12) using
1883 atoms
average map value = 0.05726, steps = 204
shifted from previous position = 18.9
rotated from previous position = 30.2 degrees
atoms outside contour = 1095, contour level = 0.06229
Position of 5a0c (#7) relative to cryosparc_P371_J916_map.mrc z flip (#12)
coordinates:
Matrix rotation and translation
-0.89591156 -0.08748371 -0.43553310 147.09781032
0.42229009 -0.47204043 -0.77385329 138.97672191
-0.13788968 -0.87722542 0.45984998 149.26233444
Axis -0.17249142 -0.49666131 0.85063168
Axis point 74.69777418 126.82872456 0.00000000
Rotation angle (degrees) 162.56376196
Shift along axis 32.56979814
> show #!1 models
> hide #7 models
> show #7 models
> volume #11 level 0.05033
> volume #12 level 0.08057
> open /Users/apple/Downloads/cryosparc_P371_J919_class_00_final_volume.mrc
Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size
128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32
> transparency #18 50
> transparency #13 50
> hide #!13 models
> hide #7 models
> hide #!6 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> hide #!1 models
> show #7 models
> show #!8 models
> hide #!8 models
> show #!1 models
> show #!13 models
> show #!4 models
> hide #!4 models
> show #5 models
> hide #5 models
> show #!6 models
> hide #!6 models
> save /Users/apple/Downloads/csparc.cxs includeMaps true
——— End of log from Fri Nov 28 18:17:17 2025 ———
opened ChimeraX session
> hide #!13 models
> open /Users/apple/Downloads/cryosparc_P371_J937_003_volume_map.mrc
Opened cryosparc_P371_J937_003_volume_map.mrc as #14, grid size 300,300,300,
pixel 0.867, shown at level 0.0245, step 2, values float32
> volume flip #14 axis z
Opened cryosparc_P371_J937_003_volume_map.mrc z flip as #15, grid size
300,300,300, pixel 0.867, shown at step 1, values float32
> hide #!15 models
> hide #!1 models
> show #!1 models
> combine #1 close false
> hide #!1 models
> show #!6 models
> combine #6 close false
> combine #7 close false
> hide #7 models
> hide #!6 models
> hide #!3 models
> show #!15 models
> transparency #15 50
> volume #15 level 0.07742
> hide #!17 models
> hide #18 models
> hide #!16 models
> show #!16 models
> show #!17 models
> show #18 models
> select add #16
2975 atoms, 2968 bonds, 437 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.38245,0.10992,-0.91742,194.95,0.077506,-0.98558,-0.15039,187,-0.92072,-0.12862,0.36841,167.53
> view matrix models
> #16,-0.38245,0.10992,-0.91742,191.4,0.077506,-0.98558,-0.15039,187.17,-0.92072,-0.12862,0.36841,156.11
> view matrix models
> #16,-0.014922,0.064965,-0.99778,175.36,0.069994,-0.99537,-0.065855,183.33,-0.99744,-0.070821,0.010305,178.28
> hide #!17 models
> view matrix models
> #16,-0.014922,0.064965,-0.99778,182.37,0.069994,-0.99537,-0.065855,183.4,-0.99744,-0.070821,0.010305,175.03
> view matrix models
> #16,0.94124,0.016979,-0.33731,85.904,0.1062,-0.96295,0.24788,160.88,-0.32061,-0.26914,-0.90817,197.31
> view matrix models
> #16,0.6158,0.19853,0.76248,31.693,-0.013436,-0.96495,0.26209,167.81,0.78779,-0.17164,-0.59155,102.23
> view matrix models
> #16,-0.056736,0.045988,0.99733,70.269,-0.1345,-0.99018,0.038008,190.1,0.98929,-0.13198,0.062364,48.953
> view matrix models
> #16,-0.056736,0.045988,0.99733,68.694,-0.1345,-0.99018,0.038008,189.37,0.98929,-0.13198,0.062364,47.206
> ui tool show "Fit in Map"
> fitmap #16 inMap #15
Fit molecule copy of 1ezx (#16) to map cryosparc_P371_J937_003_volume_map.mrc
z flip (#15) using 2975 atoms
average map value = 0.08682, steps = 136
shifted from previous position = 1.54
rotated from previous position = 27.4 degrees
atoms outside contour = 1268, contour level = 0.077423
Position of copy of 1ezx (#16) relative to
cryosparc_P371_J937_003_volume_map.mrc z flip (#15) coordinates:
Matrix rotation and translation
0.36221471 -0.11330418 0.92518250 57.47272519
-0.01922981 -0.99328137 -0.11411544 191.48317940
0.93189630 0.02354321 -0.36195994 67.99746912
Axis 0.82495481 -0.04023415 0.56376482
Axis point 0.00000000 96.53522281 19.29015841
Rotation angle (degrees) 175.21401689
Shift along axis 78.04281848
> show #!17 models
> select subtract #16
Nothing selected
> select add #17
3190 atoms, 3270 bonds, 2 pseudobonds, 422 residues, 3 models selected
> view matrix models
> #17,-0.14524,0.98625,-0.078838,137.46,-0.95305,-0.11806,0.27883,132.77,0.26569,0.11563,0.9571,127.09
> view matrix models
> #17,0.35108,0.87998,0.31997,116.61,0.41428,-0.45244,0.78973,93.952,0.83971,-0.14471,-0.5234,164.49
> view matrix models
> #17,0.54911,0.70874,-0.44291,137.73,0.78853,-0.61496,-0.0064507,113,-0.27694,-0.3457,-0.89655,196.5
> view matrix models
> #17,0.54911,0.70874,-0.44291,134.48,0.78853,-0.61496,-0.0064507,113.87,-0.27694,-0.3457,-0.89655,190.34
> view matrix models
> #17,0.9378,-0.11961,-0.32592,126.95,-0.057609,-0.97937,0.19367,123.71,-0.34236,-0.16285,-0.92535,191.74
> view matrix models
> #17,0.3628,-0.93186,-0.0012508,129.72,-0.91856,-0.35785,0.16792,137.38,-0.15693,-0.059774,-0.9858,190.03
> view matrix models
> #17,-0.40726,-0.90893,0.089337,140.28,-0.91297,0.40784,-0.012447,140.22,-0.025122,-0.086631,-0.99592,188.13
> view matrix models
> #17,-0.40726,-0.90893,0.089337,140.76,-0.91297,0.40784,-0.012447,134.78,-0.025122,-0.086631,-0.99592,187.94
> view matrix models
> #17,-0.073903,-0.92576,-0.37083,149.44,-0.76049,-0.18823,0.62147,114.32,-0.64513,0.32794,-0.69012,187.71
> view matrix models
> #17,-0.013726,-0.97437,-0.22454,143.96,-0.96969,-0.041822,0.24075,129.42,-0.24397,0.22104,-0.94426,189.05
> view matrix models
> #17,-0.13546,-0.99065,0.016086,138.59,-0.95193,0.13463,0.27516,127.4,-0.27475,0.02196,-0.96126,190.84
> view matrix models
> #17,-0.13546,-0.99065,0.016086,134.75,-0.95193,0.13463,0.27516,129.71,-0.27475,0.02196,-0.96126,190.41
> view matrix models
> #17,-0.13546,-0.99065,0.016086,134.74,-0.95193,0.13463,0.27516,129.59,-0.27475,0.02196,-0.96126,189.59
> fitmap #17 inMap #15
Fit molecule copy of 3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb (#17) to
map cryosparc_P371_J937_003_volume_map.mrc z flip (#15) using 3190 atoms
average map value = 0.08611, steps = 92
shifted from previous position = 1.81
rotated from previous position = 13.7 degrees
atoms outside contour = 1360, contour level = 0.077423
Position of copy of 3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb (#17)
relative to cryosparc_P371_J937_003_volume_map.mrc z flip (#15) coordinates:
Matrix rotation and translation
0.06326154 -0.99140205 0.11454237 128.16146514
-0.92943347 -0.01671960 0.36861077 128.17971107
-0.36352637 -0.12977839 -0.92249995 190.93357303
Axis -0.71877784 0.68947168 0.08937122
Axis point 0.00000000 149.17005870 88.62629203
Rotation angle (degrees) 159.71487953
Shift along axis 13.32062667
> select subtract #17
Nothing selected
> select add #18
1883 atoms, 1745 bonds, 394 residues, 1 model selected
> view matrix models
> #18,-0.26486,0.8524,-0.45085,130.11,0.42774,-0.31518,-0.84718,156.88,-0.86423,-0.41723,-0.28112,157.69
> view matrix models
> #18,-0.26486,0.8524,-0.45085,127.04,0.42774,-0.31518,-0.84718,159.13,-0.86423,-0.41723,-0.28112,133.82
> view matrix models
> #18,0.36105,0.83492,0.4154,114.71,0.60304,0.13074,-0.78692,152.96,-0.71132,0.53462,-0.45629,125.04
> show #!8 models
> select up
26260 atoms, 26186 bonds, 3972 residues, 27 models selected
> select up
26260 atoms, 26186 bonds, 3972 residues, 27 models selected
> select down
1883 atoms, 1745 bonds, 394 residues, 1 model selected
> select down
1883 atoms, 1745 bonds, 394 residues, 1 model selected
> combine #8 close false
> hide #!8 models
> select subtract #18
Nothing selected
> mmaker #19 to #16
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 copy of 1ezx, chain A (#16) with copy of 1ezx, chain A (#19),
sequence alignment score = 1734
RMSD between 335 pruned atom pairs is 0.000 angstroms; (across all 335 pairs:
0.000)
> hide #!16 models
> show #!16 models
> mmaker #18 to #19
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 copy of 1ezx, chain C (#19) with copy of 5a0c, chain A (#18),
sequence alignment score = 241.2
RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
3.073)
> hide #!19 models
> show #!19 models
> hide #18 models
> show #18 models
> hide #!15 models
> show #!15 models
> volume #15 level 0.06266
> combine #18 close false
> hide #!19 models
> hide #18 models
> select add #20
1883 atoms, 1745 bonds, 394 residues, 1 model selected
> view matrix models
> #20,0.93703,-0.32924,0.11649,110.54,-0.085791,-0.54033,-0.83707,168.71,0.33854,0.77436,-0.53456,110.95
> fitmap #20 inMap #15
Fit molecule copy of copy of 5a0c (#20) to map
cryosparc_P371_J937_003_volume_map.mrc z flip (#15) using 1883 atoms
average map value = 0.05371, steps = 112
shifted from previous position = 3.05
rotated from previous position = 21.1 degrees
atoms outside contour = 1163, contour level = 0.062657
Position of copy of copy of 5a0c (#20) relative to
cryosparc_P371_J937_003_volume_map.mrc z flip (#15) coordinates:
Matrix rotation and translation
0.82283210 -0.54792418 -0.15075286 115.81404414
-0.42467040 -0.41658213 -0.80381240 174.25196583
0.37762731 0.72542292 -0.57546433 108.00195017
Axis 0.94244068 -0.32563135 0.07595913
Axis point 0.00000000 79.04749924 102.02767242
Rotation angle (degrees) 125.77524387
Shift along axis 60.60969773
> volume #15 level 0.07496
> volume #15 level 0.102
> fitmap #20 inMap #15
Fit molecule copy of copy of 5a0c (#20) to map
cryosparc_P371_J937_003_volume_map.mrc z flip (#15) using 1883 atoms
average map value = 0.05371, steps = 40
shifted from previous position = 0.00581
rotated from previous position = 0.0038 degrees
atoms outside contour = 1822, contour level = 0.10203
Position of copy of copy of 5a0c (#20) relative to
cryosparc_P371_J937_003_volume_map.mrc z flip (#15) coordinates:
Matrix rotation and translation
0.82283660 -0.54793499 -0.15068899 115.81020155
-0.42463523 -0.41661833 -0.80381222 174.25584664
0.37765705 0.72539397 -0.57548131 108.00286277
Axis 0.94244310 -0.32561736 0.07598910
Axis point 0.00000000 79.04924478 102.02529443
Rotation angle (degrees) 125.77696296
Shift along axis 60.61083741
> volume #15 level 0.08481
> select #20/Ser195
Nothing selected
> ui tool show "Show Sequence Viewer"
> sequence chain #7/A #18/A #20/A
Alignment identifier is 1
> select #7/A:157 #18/A:157 #20/A:157
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #7/A:157 #18/A:157 #20/A:157
18 atoms, 15 bonds, 3 residues, 3 models selected
NEUTROPHIL ELASTASE [ID: 1] region 3 chains [138] RMSD: 42.465
> show #18 models
> hide #20 models
> select #7/A:157 #18/A:157 #20/A:157
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #7/A:157 #18/A:157 #20/A:157
18 atoms, 15 bonds, 3 residues, 3 models selected
NEUTROPHIL ELASTASE [ID: 1] region 3 chains [138] RMSD: 42.465
> select #7/A:195 #18/A:195 #20/A:195
15 atoms, 12 bonds, 3 residues, 3 models selected
> select #7/A:195 #18/A:195 #20/A:195
15 atoms, 12 bonds, 3 residues, 3 models selected
NEUTROPHIL ELASTASE [ID: 1] region 3 chains [166] RMSD: 29.400
> show #!19 models
> hide #!15 models
> select #7/A:195 #18/A:195 #20/A:195
15 atoms, 12 bonds, 3 residues, 3 models selected
> select #7/A:195 #18/A:195 #20/A:195
15 atoms, 12 bonds, 3 residues, 3 models selected
> select #7/A:195-198 #18/A:195-198 #20/A:195-198
66 atoms, 63 bonds, 12 residues, 3 models selected
NEUTROPHIL ELASTASE [ID: 1] region 3 chains [166-169] RMSD: 25.331
> select #7/A:196 #18/A:196 #20/A:196
12 atoms, 9 bonds, 3 residues, 3 models selected
> select #7/A:195-196 #18/A:195-196 #20/A:195-196
27 atoms, 24 bonds, 6 residues, 3 models selected
NEUTROPHIL ELASTASE [ID: 1] region 3 chains [166-167] RMSD: 26.853
> hide #18 models
> ui tool show "Show Sequence Viewer"
> sequence chain #8/C #19/C
Alignment identifier is 2
> select #7/A:202 #18/A:202 #20/A:202
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #7/A:202 #18/A:202 #20/A:202
18 atoms, 15 bonds, 3 residues, 3 models selected
NEUTROPHIL ELASTASE [ID: 1] region 3 chains [173] RMSD: 20.338
> show #18 models
> hide #!19 models
> show #20 models
> hide #18 models
> show #!15 models
> fitmap #20 inMap #15
Fit molecule copy of copy of 5a0c (#20) to map
cryosparc_P371_J937_003_volume_map.mrc z flip (#15) using 1883 atoms
average map value = 0.05371, steps = 44
shifted from previous position = 0.00953
rotated from previous position = 0.0167 degrees
atoms outside contour = 1647, contour level = 0.084806
Position of copy of copy of 5a0c (#20) relative to
cryosparc_P371_J937_003_volume_map.mrc z flip (#15) coordinates:
Matrix rotation and translation
0.82274117 -0.54810241 -0.15060115 115.80769501
-0.42459237 -0.41645168 -0.80392121 174.26154718
0.37791306 0.72536318 -0.57535204 108.00158372
Axis 0.94240739 -0.32569200 0.07611192
Axis point 0.00000000 79.05386504 102.02910751
Rotation angle (degrees) 125.76988347
Shift along axis 60.60264436
> save /Users/apple/Downloads/csparc.cxs
> show #!19 models
> hide #20 models
> show #20 models
> hide #!19 models
> save /Users/apple/Downloads/csparc.cxs includeMaps true
> open /Users/apple/Downloads/cryosparc_P371_J936_volume_map.mrc
Opened cryosparc_P371_J936_volume_map.mrc as #21, grid size 300,300,300, pixel
0.867, shown at level 0.0323, step 2, values float32
> volume #21 level 0.05076
> volume flip #21 axis z
Opened cryosparc_P371_J936_volume_map.mrc z flip as #22, grid size
300,300,300, pixel 0.867, shown at step 1, values float32
> transparency #22 50
> volume #22 level 0.08397
> hide #!15 models
> hide #!22 models
> show #!22 models
> volume #22 level 0.09518
> select add #21
18 atoms, 15 bonds, 3 residues, 5 models selected
> select subtract #21
18 atoms, 15 bonds, 3 residues, 3 models selected
> close #21-22
> show #!15 models
> volume #15 level 0.06828
> show #!19 models
> hide #!19 models
> show #!19 models
> select up
309 atoms, 309 bonds, 45 residues, 3 models selected
> select up
4908 atoms, 5010 bonds, 654 residues, 3 models selected
> select down
309 atoms, 309 bonds, 45 residues, 3 models selected
> select down
18 atoms, 15 bonds, 3 residues, 3 models selected
> mmaker #20 to #19
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 copy of 1ezx, chain C (#19) with copy of copy of 5a0c, chain A
(#20), sequence alignment score = 241.2
RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
3.073)
> fitmap #20 inMap #15
Fit molecule copy of copy of 5a0c (#20) to map
cryosparc_P371_J937_003_volume_map.mrc z flip (#15) using 1883 atoms
average map value = 0.05371, steps = 112
shifted from previous position = 3.64
rotated from previous position = 21.1 degrees
atoms outside contour = 1322, contour level = 0.068282
Position of copy of copy of 5a0c (#20) relative to
cryosparc_P371_J937_003_volume_map.mrc z flip (#15) coordinates:
Matrix rotation and translation
0.82286685 -0.54787123 -0.15075561 115.81112827
-0.42466982 -0.41665469 -0.80377510 174.25405615
0.37755223 0.72542124 -0.57551571 108.00346093
Axis 0.94245398 -0.32559967 0.07592986
Axis point 0.00000000 79.04723098 102.02619388
Rotation angle (degrees) 125.77839312
Shift along axis 60.61028363
> hide #!19 models
> show #18 models
> hide #18 models
> color #20 #ff9cd5ff
> open /Users/apple/Downloads/cryosparc_P371_J948_003_volume_map.mrc
Opened cryosparc_P371_J948_003_volume_map.mrc as #21, grid size 300,300,300,
pixel 0.867, shown at level 0.0208, step 2, values float32
> volume flip #21 axis z
Opened cryosparc_P371_J948_003_volume_map.mrc z flip as #22, grid size
300,300,300, pixel 0.867, shown at step 1, values float32
> select add #22
18 atoms, 15 bonds, 3 residues, 5 models selected
> select subtract #22
18 atoms, 15 bonds, 3 residues, 3 models selected
> hide #20 models
> show #20 models
> hide #20 models
> show #20 models
> hide #20 models
> hide #!17 models
> hide #!16 models
> select add #18
1895 atoms, 1755 bonds, 396 residues, 3 models selected
> select subtract #18
12 atoms, 10 bonds, 2 residues, 2 models selected
> select add #20
1889 atoms, 1750 bonds, 395 residues, 2 models selected
> select subtract #20
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #7
1883 atoms, 1745 bonds, 394 residues, 1 model selected
> select subtract #7
Nothing selected
> volume #22 level 0.07591
> select down
Nothing selected
> combine #16 close false
> combine #17 close false
> combine #118 close false
No structures specified
> combine #18 close false
> combine #19 close false
> transparency #22 50
> hide #!26 models
> hide #25 models
> hide #!24 models
> select add #23
2975 atoms, 2968 bonds, 437 residues, 1 model selected
> view matrix models
> #23,0.36221,-0.1133,0.92518,56.114,-0.01923,-0.99328,-0.11412,190.58,0.9319,0.023543,-0.36196,109.58
> view matrix models
> #23,0.36479,-0.4655,-0.80637,178.05,-0.26782,-0.88191,0.38795,170.47,-0.89174,0.074435,-0.44638,227.76
> view matrix models
> #23,0.44719,-0.25874,-0.8562,163.07,-0.021132,-0.96003,0.27908,165.82,-0.89419,-0.10671,-0.43478,238.29
> fitmap #23 inMap #22
Fit molecule copy of copy of 1ezx (#23) to map
cryosparc_P371_J948_003_volume_map.mrc z flip (#22) using 2975 atoms
average map value = 0.09755, steps = 212
shifted from previous position = 6.95
rotated from previous position = 52.1 degrees
atoms outside contour = 1049, contour level = 0.075909
Position of copy of copy of 1ezx (#23) relative to
cryosparc_P371_J948_003_volume_map.mrc z flip (#22) coordinates:
Matrix rotation and translation
-0.35370767 0.06701706 -0.93295209 204.77529060
0.13164154 -0.98393545 -0.12058828 178.13445921
-0.92604610 -0.16546825 0.33920329 197.74865607
Axis -0.56822714 -0.08743693 0.81821311
Axis point 168.87143840 102.30996261 0.00000000
Rotation angle (degrees) 177.73673097
Shift along axis 29.86613558
> show #!24 models
> select subtract #23
Nothing selected
> select add #24
3190 atoms, 3270 bonds, 2 pseudobonds, 422 residues, 3 models selected
> view matrix models
> #24,0.063262,-0.9914,0.11454,130.74,-0.92943,-0.01672,0.36861,129.85,-0.36353,-0.12978,-0.9225,142.93
> view matrix models
> #24,-0.096416,0.97724,-0.18895,136.05,-0.93565,-0.024237,0.35209,130.5,0.33949,0.21074,0.9167,71.599
> fitmap #24 inMap #22
Fit molecule copy of copy of 3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb
(#24) to map cryosparc_P371_J948_003_volume_map.mrc z flip (#22) using 3190
atoms
average map value = 0.0891, steps = 132
shifted from previous position = 5.66
rotated from previous position = 8.17 degrees
atoms outside contour = 1367, contour level = 0.075909
Position of copy of copy of 3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb
(#24) relative to cryosparc_P371_J948_003_volume_map.mrc z flip (#22)
coordinates:
Matrix rotation and translation
-0.11543452 0.98844688 -0.09822239 132.09657369
-0.96240593 -0.08681878 0.25736612 135.79332431
0.24586519 0.12423874 0.96130902 66.63288452
Axis -0.06705205 -0.17330603 -0.98258284
Axis point 117.34974721 5.42399614 0.00000000
Rotation angle (degrees) 96.91935179
Shift along axis -97.86347693
> select subtract #24
Nothing selected
> show #25 models
> hide #25 models
> show #!26 models
> mmaker #26 to #23
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 copy of copy of 1ezx, chain A (#23) with copy of copy of 1ezx,
chain A (#26), sequence alignment score = 1734
RMSD between 335 pruned atom pairs is 0.000 angstroms; (across all 335 pairs:
0.000)
> hide #!24 models
> show #!24 models
> hide #!23 models
> show #25 models
> mmaker #25 to #26
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 copy of copy of 1ezx, chain C (#26) with copy of copy of 5a0c,
chain A (#25), sequence alignment score = 241.2
RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
3.073)
> hide #!26 models
> fitmap #25 inMap #22
Fit molecule copy of copy of 5a0c (#25) to map
cryosparc_P371_J948_003_volume_map.mrc z flip (#22) using 1883 atoms
average map value = 0.05123, steps = 108
shifted from previous position = 4.84
rotated from previous position = 10.8 degrees
atoms outside contour = 1517, contour level = 0.075909
Position of copy of copy of 5a0c (#25) relative to
cryosparc_P371_J948_003_volume_map.mrc z flip (#22) coordinates:
Matrix rotation and translation
-0.96845122 0.24832236 -0.02093422 151.81572996
-0.06074205 -0.31669183 -0.94658158 164.61638030
-0.24168707 -0.91544650 0.32178420 153.13479473
Axis 0.08170221 0.57928205 -0.81102223
Axis point 93.94357397 127.91849703 0.00000000
Rotation angle (degrees) 169.01569846
Shift along axis -16.43272779
> select add #25
1883 atoms, 1745 bonds, 394 residues, 1 model selected
> view matrix models
> #25,-0.77469,0.63129,-0.036468,145.91,-0.26885,-0.38101,-0.88462,168.48,-0.57235,-0.6755,0.46489,156.84
> select subtract #25
Nothing selected
> show #!26 models
> hide #!24 models
> show #!24 models
> hide #25 models
> mmaker #25 to #26
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 copy of copy of 1ezx, chain C (#26) with copy of copy of 5a0c,
chain A (#25), sequence alignment score = 241.2
RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
3.073)
> hide #!26 models
> show #25 models
> show #!26 models
> mmaker #25 to #26
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 copy of copy of 1ezx, chain C (#26) with copy of copy of 5a0c,
chain A (#25), sequence alignment score = 241.2
RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
3.073)
> show #!23 models
> hide #!23 models
> hide #!26 models
> hide #25 models
> show #!26 models
> hide #!26 models
> show #25 models
> hide #25 models
> show #25 models
> show #!26 models
> select add #25
1883 atoms, 1745 bonds, 394 residues, 1 model selected
> view matrix models
> #25,-0.9367,0.31111,-0.16061,148.23,0.0082594,-0.43896,-0.89847,161.81,-0.35002,-0.84292,0.40861,148.72
> mmaker #25 to #26
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 copy of copy of 1ezx, chain C (#26) with copy of copy of 5a0c,
chain A (#25), sequence alignment score = 241.2
RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
3.073)
> hide #!22 models
> hide #!26 models
> select subtract #25
Nothing selected
> show #!22 models
> hide #!22 models
> show #!26 models
> hide #25 models
> show #25 models
> hide #25 models
> show #25 models
> select add #25
1883 atoms, 1745 bonds, 394 residues, 1 model selected
> view matrix models
> #25,-0.9367,0.31111,-0.16061,148.98,0.0082594,-0.43896,-0.89847,185.49,-0.35002,-0.84292,0.40861,135.78
> view matrix models
> #25,-0.94082,0.30916,-0.13882,149.02,0.0018899,-0.40484,-0.91439,185.4,-0.33889,-0.86054,0.3803,135.77
> view matrix models
> #25,-0.94082,0.30916,-0.13882,149.87,0.0018899,-0.40484,-0.91439,185.44,-0.33889,-0.86054,0.3803,134.62
> view matrix models
> #25,0.61831,0.086644,0.78114,122.91,0.644,0.51386,-0.56675,167.46,-0.45051,0.85348,0.26193,124.99
> view matrix models
> #25,0.68702,0.1216,0.7164,121.63,0.51681,0.61128,-0.59937,169.03,-0.5108,0.78202,0.35712,126.32
> view matrix models
> #25,-0.95703,-0.21929,0.18975,153.1,-0.15891,-0.15078,-0.97571,186.56,0.24258,-0.96394,0.10945,125.96
> select #8/C:202 #19/C:202
12 atoms, 10 bonds, 2 residues, 2 models selected
> select #8/C:202 #19/C:202
12 atoms, 10 bonds, 2 residues, 2 models selected
TRYPSIN [ID: 2] region 2 chains [204] RMSD: 14.654
> select #8/C:195 #19/C:195
12 atoms, 10 bonds, 2 residues, 2 models selected
> select #8/C:195 #19/C:195
12 atoms, 10 bonds, 2 residues, 2 models selected
TRYPSIN [ID: 2] region 2 chains [197] RMSD: 26.141
> select #7/A:202 #18/A:202 #20/A:202
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #7/A:202 #18/A:202 #20/A:202
18 atoms, 15 bonds, 3 residues, 3 models selected
NEUTROPHIL ELASTASE [ID: 1] region 3 chains [173] RMSD: 20.338
> show #20 models
> hide #20 models
> select #25/A Ser 202
Expected a keyword
> select #25/A:Ser 202
Expected a keyword
> select #25/A:Ser202
Nothing selected
> select #25: 202.A
Expected an objects specifier or a keyword
> select #25/A: 202
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #25
1883 atoms, 1745 bonds, 394 residues, 1 model selected
> select subtract #25
Nothing selected
> select add #25
1883 atoms, 1745 bonds, 394 residues, 1 model selected
> hide #!26 models
> show #!22 models
> show #!21 models
> hide #!21 models
> show #!23 models
> view matrix models
> #25,-0.95703,-0.21929,0.18975,145.87,-0.15891,-0.15078,-0.97571,168.63,0.24258,-0.96394,0.10945,142.99
> view matrix models
> #25,-0.92453,-0.26838,-0.2706,146.59,0.26503,0.057502,-0.96252,159.94,0.27389,-0.96159,0.017967,142.62
> select #25/A: 202
6 atoms, 5 bonds, 1 residue, 1 model selected
> fitmap #25 inMap #22
Fit molecule copy of copy of 5a0c (#25) to map
cryosparc_P371_J948_003_volume_map.mrc z flip (#22) using 1883 atoms
average map value = 0.05191, steps = 80
shifted from previous position = 6.32
rotated from previous position = 2.92 degrees
atoms outside contour = 1497, contour level = 0.075909
Position of copy of copy of 5a0c (#25) relative to
cryosparc_P371_J948_003_volume_map.mrc z flip (#22) coordinates:
Matrix rotation and translation
-0.92706110 -0.29700612 -0.22879047 151.40778359
0.22401549 0.05050483 -0.97327608 156.79876717
0.30062397 -0.95353900 0.01971291 143.82999540
Axis 0.02656202 -0.71248224 0.70118722
Axis point 58.53175465 0.00000000 169.56684388
Rotation angle (degrees) 158.19010570
Shift along axis -6.84288466
> hide #!22 models
> show #!22 models
> view
> ui mousemode right "tape measure"
> marker segment #27 position 135.4,127.7,167.7 toPosition 124.3,129.1,64.78
> color yellow radius 0.2167 label 103.5 labelHeight 10.35 labelColor yellow
> marker segment #27 position 125.5,89.39,147.8 toPosition 125.6,178.4,143.9
> color yellow radius 0.2167 label 89.07 labelHeight 8.907 labelColor yellow
> close #27
> save /Users/apple/Downloads/csparc.cxs includeMaps true
> open 1oph fromDatabase pdb format mmcif
1oph title:
Non-covalent complex between α-1-π-pittsburgh and S195A trypsin [more info...]
Chain information for 1oph #27
---
Chain | Description | UniProt
A | Alpha-1-antitrypsin precursor | A1AT_HUMAN 1-394
B | Trypsinogen, cationic precursor | TRY1_BOVIN -4-245
1oph mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| software_defined_assembly
> select #27/A
3121 atoms, 2980 bonds, 578 residues, 1 model selected
> delete #27/A
> mmaker #27 to #26
Computing secondary structure
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 copy of copy of 1ezx, chain C (#26) with 1oph, chain B (#27),
sequence alignment score = 997.3
RMSD between 122 pruned atom pairs is 0.798 angstroms; (across all 140 pairs:
2.232)
> show #!26 models
> hide #25 models
> hide #!26 models
> select add #27
1798 atoms, 1661 bonds, 397 residues, 1 model selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #27,-0.045437,0.97583,0.21376,84.546,-0.056484,-0.21614,0.97473,106.46,0.99737,0.032215,0.06494,111.78
> view matrix models
> #27,-0.045437,0.97583,0.21376,84.655,-0.056484,-0.21614,0.97473,107.21,0.99737,0.032215,0.06494,111.79
> view matrix models
> #27,-0.028766,0.99015,0.13706,88.816,-0.25704,-0.13983,0.95623,110.79,0.96597,-0.0077222,0.25853,101.15
> hide #27 models
> show #25 models
> show #27 models
> hide #25 models
> fitmap #27 inMap #22
Fit molecule 1oph (#27) to map cryosparc_P371_J948_003_volume_map.mrc z flip
(#22) using 1798 atoms
average map value = 0.05191, steps = 140
shifted from previous position = 5.08
rotated from previous position = 28.4 degrees
atoms outside contour = 1427, contour level = 0.075909
Position of 1oph (#27) relative to cryosparc_P371_J948_003_volume_map.mrc z
flip (#22) coordinates:
Matrix rotation and translation
0.00693020 0.97101511 -0.23891762 117.08280460
0.05673053 0.23815679 0.96956846 87.39953806
0.99836547 -0.02027323 -0.05343572 123.84959279
Axis -0.54108517 -0.67634607 -0.49978278
Axis point 8.31144747 0.00000000 37.97716599
Rotation angle (degrees) 113.83939914
Shift along axis -184.36199747
> ui tool show "Show Sequence Viewer"
> sequence chain #27/B
Alignment identifier is 27/B
> select #27/B:195
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #27/B:195
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide #27 models
> select add #27
1798 atoms, 1661 bonds, 397 residues, 1 model selected
> show #25 models
> show #!26 models
> hide #25 models
> hide #!26 models
> show #!26 models
> select up
45957 atoms, 45539 bonds, 7200 residues, 38 models selected
> select up
45957 atoms, 45539 bonds, 7200 residues, 38 models selected
> select down
1798 atoms, 1661 bonds, 397 residues, 1 model selected
> select down
1798 atoms, 1661 bonds, 397 residues, 1 model selected
> select down
1798 atoms, 1661 bonds, 397 residues, 1 model selected
> select #25/A: 202
6 atoms, 5 bonds, 1 residue, 1 model selected
> show #25 models
> hide #25 models
> select add #25
1883 atoms, 1745 bonds, 394 residues, 1 model selected
> select #26/B: 195
Nothing selected
> select #26/A: 195
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide #!22 models
> select #26/C: 195
6 atoms, 5 bonds, 1 residue, 1 model selected
> style sel ball
Changed 6 atom styles
> show sel atoms
> show #25 models
> hide #!26 models
> select #25/A: 202
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 6 atom styles
> style sel sphere
Changed 6 atom styles
> style sel ball
Changed 6 atom styles
> select add #25
1883 atoms, 1745 bonds, 394 residues, 1 model selected
> select subtract #25
Nothing selected
> select #23/A: 358
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 8 atom styles
> style sel stick
Changed 8 atom styles
> style sel ball
Changed 8 atom styles
> rainbow sel
> style sel ball
Changed 8 atom styles
> rainbow sel
> select add #23
2975 atoms, 2968 bonds, 437 residues, 1 model selected
> select subtract #23
Nothing selected
> show #!22 models
> hide #25 models
> show #!26 models
> hide #!26 models
> show #25 models
> hide #25 models
> volume #22 level 0.09375
> show #25 models
> hide #25 models
> show #!26 models
> hide #!26 models
> show #25 models
> hide #25 models
> open /Users/apple/Downloads/cryosparc_P371_J950_050_class_averages.mrc
Opened cryosparc_P371_J950_050_class_averages.mrc as #28, grid size
256,256,200, pixel 1.02,1.02,1.02, shown at level 0.251, step 1, values
float32
> close #28
> show #25 models
> select #25/A: 358
Nothing selected
> select #25/A: 202
6 atoms, 5 bonds, 1 residue, 1 model selected
> show #!26 models
> hide #!26 models
> hide #25 models
> hide #!24 models
> hide #!23 models
> show #!26 models
> hide #!22 models
> show #!22 models
> show #25 models
> hide #25 models
> hide #!26 models
> show #25 models
> show #!23 models
> ui mousemode right "mark center"
> marker #28 position 123.2,156.9,145.8 color yellow radius 1
> marker #28 position 123.8,156.1,145.9 color yellow radius 1
> marker #28 position 124.3,155.3,145.5 color yellow radius 1
> marker #28 position 125.1,154.7,145.3 color yellow radius 1
> marker #28 position 133.4,155.3,146.7 color yellow radius 1
> close #28
> marker #28 position 138.7,150.2,141.7 color yellow radius 1
> ui mousemode right "translate selected models"
> view matrix models #28,1,0,0,-3.5551,0,1,0,1.3867,0,0,1,-2.5059
> view matrix models #28,1,0,0,-9.6384,0,1,0,2.0334,0,0,1,1.97
> view matrix models #28,1,0,0,-10.982,0,1,0,2.5507,0,0,1,3.0554
> view matrix models #28,1,0,0,-10.831,0,1,0,1.6826,0,0,1,8.0306
> view matrix models #28,1,0,0,-9.3846,0,1,0,2.9816,0,0,1,8.0266
> view matrix models #28,1,0,0,-8.1692,0,1,0,2.6506,0,0,1,8.3086
> save /Users/apple/Downloads/csparc.cxs includeMaps true
——— End of log from Wed Dec 10 00:50:43 2025 ———
opened ChimeraX session
> open /Users/apple/Downloads/cryosparc_P371_J1081_flex_map.mrc
Opened cryosparc_P371_J1081_flex_map.mrc as #29, grid size 300,300,300, pixel
0.867, shown at level 0.000695, step 2, values float32
> open /Users/apple/Downloads/cryosparc_P371_J1081_noflex_map.mrc
Opened cryosparc_P371_J1081_noflex_map.mrc as #30, grid size 300,300,300,
pixel 0.867, shown at level 0.000724, step 2, values float32
> select subtract #28
Nothing selected
> hide #28 models
> hide #25 models
> hide #!23 models
> hide #!22 models
> volume #29 level 0.002147
> volume #30 level 0.002175
> volume #29 level 0.003511
> transparency #29 50
> combine #23 close false
> select #31
2975 atoms, 2968 bonds, 437 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #31,0.50304,0.85251,0.14206,39.723,-0.75321,0.51304,-0.41165,160.2,-0.42382,0.10008,0.9002,116.9
> view matrix models
> #31,-0.21174,-0.30564,-0.9283,218.18,-0.38185,0.90021,-0.2093,101.13,0.89964,0.31016,-0.30733,89.797
> view matrix models
> #31,-0.21174,-0.30564,-0.9283,229.13,-0.38185,0.90021,-0.2093,126.74,0.89964,0.31016,-0.30733,63.57
> view matrix models
> #31,-0.62266,-0.60519,-0.49602,248.5,-0.47185,0.79608,-0.37898,148.7,0.62422,-0.0019301,-0.78124,127.72
> view matrix models
> #31,-0.0049269,-0.1605,-0.98702,210.49,-0.17098,0.97264,-0.15731,105.85,0.98526,0.16799,-0.032234,50.793
> view matrix models
> #31,-0.0049269,-0.1605,-0.98702,193.82,-0.17098,0.97264,-0.15731,100.89,0.98526,0.16799,-0.032234,45.314
> ui tool show "Fit to Segments"
> ui tool show "Fit in Map"
> fitmap #31 inMap #29
Fit molecule copy of copy of copy of 1ezx (#31) to map
cryosparc_P371_J1081_flex_map.mrc (#29) using 2975 atoms
average map value = 0.00359, steps = 168
shifted from previous position = 8.5
rotated from previous position = 22.8 degrees
atoms outside contour = 1538, contour level = 0.003511
Position of copy of copy of copy of 1ezx (#31) relative to
cryosparc_P371_J1081_flex_map.mrc (#29) coordinates:
Matrix rotation and translation
-0.34543281 0.02159528 -0.93819498 206.18704506
-0.19036417 0.97733785 0.09258621 89.05596314
0.91893289 0.21058103 -0.33349359 58.61087565
Axis 0.06300096 -0.99157607 -0.11317149
Axis point 88.67581154 0.00000000 98.10599897
Rotation angle (degrees) 110.53590433
Shift along axis -81.94885947
> combine #26 close false
> mmaker #32 to #31
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 copy of copy of copy of 1ezx, chain A (#31) with copy of copy of
copy of 1ezx, chain A (#32), sequence alignment score = 1734
RMSD between 335 pruned atom pairs is 0.000 angstroms; (across all 335 pairs:
0.000)
> volume #29 level 0.003107
> hide #!32 models
> show #!32 models
> mmaker #27 to #32
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 copy of copy of copy of 1ezx, chain C (#32) with 1oph, chain B
(#27), sequence alignment score = 997.3
RMSD between 122 pruned atom pairs is 0.798 angstroms; (across all 140 pairs:
2.232)
> show #27 models
> select subtract #31
Nothing selected
> hide #!32 models
> fitmap #27 inMap #29
Fit molecule 1oph (#27) to map cryosparc_P371_J1081_flex_map.mrc (#29) using
1798 atoms
average map value = 0.001969, steps = 84
shifted from previous position = 3.54
rotated from previous position = 2.5 degrees
atoms outside contour = 1466, contour level = 0.003107
Position of 1oph (#27) relative to cryosparc_P371_J1081_flex_map.mrc (#29)
coordinates:
Matrix rotation and translation
0.01488540 0.98783365 0.15480023 90.39787129
0.09394517 0.15275083 -0.98378935 155.00101390
-0.99546609 0.02918683 -0.09052845 143.69933185
Axis 0.57090422 0.64827970 -0.50378746
Axis point 63.02718238 0.00000000 111.05539948
Rotation angle (degrees) 117.48046157
Shift along axis 79.69861501
> select #27/A: 195
Nothing selected
> select #27/B: 195
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 5 atom styles
> rainbow sel
> color sel red
> select add #27
1798 atoms, 1661 bonds, 397 residues, 1 model selected
> select subtract #27
Nothing selected
> select add #27
1798 atoms, 1661 bonds, 397 residues, 1 model selected
> view matrix models
> #27,0.014885,0.98783,0.1548,88.407,0.093945,0.15275,-0.98379,156.95,-0.99547,0.029187,-0.090528,145.09
> view matrix models
> #27,0.50068,0.52374,0.68922,56.841,0.53814,0.43533,-0.72173,119.4,-0.67804,0.73225,-0.063887,112.1
> view matrix models
> #27,0.50068,0.52374,0.68922,56.703,0.53814,0.43533,-0.72173,120.1,-0.67804,0.73225,-0.063887,108.86
> fitmap #27 inMap #29
Fit molecule 1oph (#27) to map cryosparc_P371_J1081_flex_map.mrc (#29) using
1798 atoms
average map value = 0.002206, steps = 72
shifted from previous position = 3.25
rotated from previous position = 11.5 degrees
atoms outside contour = 1384, contour level = 0.003107
Position of 1oph (#27) relative to cryosparc_P371_J1081_flex_map.mrc (#29)
coordinates:
Matrix rotation and translation
0.43383501 0.41278377 0.80087249 57.23345510
0.54433424 0.58824117 -0.59805732 104.34070071
-0.71797452 0.69540053 0.03050727 103.99925252
Axis 0.64695257 0.75968612 0.06579798
Axis point 48.98630646 0.00000000 62.63708921
Rotation angle (degrees) 88.49342140
Shift along axis 123.13645375
> mmaker #27 to #32
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 copy of copy of copy of 1ezx, chain C (#32) with 1oph, chain B
(#27), sequence alignment score = 997.3
RMSD between 122 pruned atom pairs is 0.798 angstroms; (across all 140 pairs:
2.232)
> hide #27 models
> show #!32 models
> hide #!31 models
> volume #29 level 0.002349
> show #27 models
> color #27 #dbd548ff
> select subtract #27
Nothing selected
> select add #27
1798 atoms, 1661 bonds, 397 residues, 1 model selected
> select subtract #27
Nothing selected
> select add #32
3984 atoms, 3982 bonds, 5 pseudobonds, 592 residues, 3 models selected
> hide #!32 models
> hide #27 models
> show #28 models
> hide #28 models
> show #27 models
> select subtract #32
Nothing selected
> select add #27
1798 atoms, 1661 bonds, 397 residues, 1 model selected
> view matrix models
> #27,-0.014536,0.98302,0.18291,86.474,0.10897,0.18339,-0.97698,152.94,-0.99394,0.00573,-0.10979,145.21
> view matrix models
> #27,-0.094668,0.98683,0.13115,91.714,0.12875,0.14277,-0.98135,154.1,-0.98715,-0.076017,-0.14057,149.8
> view matrix models
> #27,-0.094668,0.98683,0.13115,93.34,0.12875,0.14277,-0.98135,151.17,-0.98715,-0.076017,-0.14057,149.26
> view matrix models
> #27,-0.22979,0.97316,0.012679,104.9,0.38456,0.10276,-0.91736,142.04,-0.89404,-0.20593,-0.39785,168.25
> view matrix models
> #27,-0.22979,0.97316,0.012679,104.93,0.38456,0.10276,-0.91736,141.75,-0.89404,-0.20593,-0.39785,167.14
> view matrix models
> #27,-0.22979,0.97316,0.012679,104.2,0.38456,0.10276,-0.91736,144.37,-0.89404,-0.20593,-0.39785,166.13
> hide #27 models
> show #27 models
> hide #27 models
> show #27 models
> view matrix models
> #27,-0.49784,0.70316,-0.50765,154.01,0.28651,-0.41914,-0.86153,160.52,-0.81858,-0.57435,0.0072046,149.92
> view matrix models
> #27,-0.29847,0.7881,-0.53834,148.31,0.35815,-0.43034,-0.82857,156.97,-0.88467,-0.44011,-0.15381,157.66
> view matrix models
> #27,-0.24543,0.58716,-0.77137,169.05,0.40215,-0.66234,-0.63212,150.71,-0.88207,-0.46535,-0.073571,153.15
> view matrix models
> #27,-0.18594,0.44822,-0.87437,179.01,0.44471,-0.75513,-0.48167,142.87,-0.87616,-0.4784,-0.058915,152.48
> view matrix models
> #27,0.22752,0.8665,-0.44432,126.63,0.092657,-0.47348,-0.87592,168.02,-0.96935,0.15812,-0.18801,142.01
> view matrix models
> #27,0.50128,0.79078,-0.35126,116.34,0.31994,-0.54657,-0.77389,158.19,-0.80396,0.27556,-0.52699,156.35
> view matrix models
> #27,0.70079,0.62982,-0.335,115.76,0.20665,-0.62869,-0.74969,162.11,-0.68278,0.45615,-0.57073,150.23
> view matrix models
> #27,0.70079,0.62982,-0.335,118.94,0.20665,-0.62869,-0.74969,162.08,-0.68278,0.45615,-0.57073,148.91
> view matrix models
> #27,-0.4262,0.53806,-0.72722,175.4,-0.24981,-0.84263,-0.47705,162.45,-0.86946,-0.021651,0.49354,99.401
> view matrix models
> #27,-0.4262,0.53806,-0.72722,174.48,-0.24981,-0.84263,-0.47705,159.2,-0.86946,-0.021651,0.49354,98.413
> hide #27 models
> select subtract #27
Nothing selected
> hide #!29 models
> show #!30 models
> show #!29 models
> hide #!29 models
> transparency #30 50
> show #!29 models
> hide #!29 models
> volume #30 level 0.002739
> show #!24 models
> hide #!24 models
> show #!6 models
> hide #!6 models
> combine #6 close false
> select add #33
3190 atoms, 3270 bonds, 2 pseudobonds, 422 residues, 3 models selected
> view matrix models
> #33,-0.12378,0.83325,-0.53886,145.44,-0.98558,-0.040107,0.16437,137.25,0.11535,0.55143,0.8262,70.943
> view matrix models
> #33,-0.12378,0.83325,-0.53886,121.31,-0.98558,-0.040107,0.16437,137.63,0.11535,0.55143,0.8262,134.88
> view matrix models
> #33,0.096483,0.85305,0.51282,84.33,-0.9177,-0.12324,0.37767,130.03,0.38537,-0.50706,0.77096,135.66
> view matrix models
> #33,0.64301,0.74737,-0.16726,96.505,-0.76213,0.64595,-0.043654,137.8,0.075414,0.15554,0.98495,132
> view matrix models
> #33,0.64301,0.74737,-0.16726,99.153,-0.76213,0.64595,-0.043654,141.43,0.075414,0.15554,0.98495,123.21
> view matrix models
> #33,0.53757,0.81725,-0.20763,102.02,-0.84165,0.53507,-0.073018,144.14,0.051423,0.214,0.97548,123.72
> view matrix models
> #33,0.56724,0.791,-0.22925,102.27,-0.77653,0.60643,0.17101,135.07,0.2743,0.081017,0.95823,120.83
> view matrix models
> #33,0.56724,0.791,-0.22925,126.45,-0.77653,0.60643,0.17101,136.72,0.2743,0.081017,0.95823,121.23
> view matrix models
> #33,0.56724,0.791,-0.22925,77.167,-0.77653,0.60643,0.17101,133.67,0.2743,0.081017,0.95823,119.95
> view matrix models
> #33,0.74297,0.64514,-0.17831,73.008,0.66921,-0.71089,0.21633,111.62,0.012799,-0.28005,-0.9599,186.09
> view matrix models
> #33,0.09813,0.99411,-0.046082,78.903,0.94172,-0.077789,0.32727,101.1,0.32175,-0.075511,-0.94381,179.45
> view matrix models
> #33,0.09813,0.99411,-0.046082,125.57,0.94172,-0.077789,0.32727,97.242,0.32175,-0.075511,-0.94381,182.15
> view matrix models
> #33,0.09813,0.99411,-0.046082,123.79,0.94172,-0.077789,0.32727,98.857,0.32175,-0.075511,-0.94381,179.28
> view matrix models
> #33,0.09813,0.99411,-0.046082,130.36,0.94172,-0.077789,0.32727,110.04,0.32175,-0.075511,-0.94381,181.04
> view matrix models
> #33,0.18807,0.98065,-0.054404,129.09,0.97234,-0.17809,0.15115,115.39,0.13853,-0.081324,-0.98701,185.63
> view matrix models
> #33,0.12584,0.98709,-0.099091,131.56,0.99196,-0.12652,-0.00060121,119.63,-0.01313,-0.098219,-0.99508,188.6
> view matrix models
> #33,0.12584,0.98709,-0.099091,132.15,0.99196,-0.12652,-0.00060121,116.48,-0.01313,-0.098219,-0.99508,193.2
> fitmap #33 inMap #29
Fit molecule copy of 3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb (#33) to
map cryosparc_P371_J1081_flex_map.mrc (#29) using 3190 atoms
average map value = 0.003475, steps = 104
shifted from previous position = 6.47
rotated from previous position = 18.9 degrees
atoms outside contour = 969, contour level = 0.0023495
Position of copy of 3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb (#33)
relative to cryosparc_P371_J1081_flex_map.mrc (#29) coordinates:
Matrix rotation and translation
-0.15475687 0.98403031 -0.08794666 131.65046804
0.97076802 0.13493018 -0.19850246 120.81278809
-0.18346579 -0.11609543 -0.97614657 191.47093637
Axis 0.64964584 0.75301343 -0.10455170
Axis point 18.09163929 0.00000000 103.49035885
Rotation angle (degrees) 176.36359820
Shift along axis 156.48121953
> select subtract #33
Nothing selected
> color #33 #dbda64ff
> show #!30 models
> hide #!29 models
> hide #!30 models
> hide #!33 models
> open /Users/apple/Downloads/cryosparc_P371_J973_003_volume_map.mrc
Opened cryosparc_P371_J973_003_volume_map.mrc as #34, grid size 300,300,300,
pixel 0.867, shown at level 0.0274, step 2, values float32
> volume #34 level 0.05742
> transparency #34 50
> show #27 models
> volume flip #34 axis z
Opened cryosparc_P371_J973_003_volume_map.mrc z flip as #35, grid size
300,300,300, pixel 0.867, shown at step 1, values float32
> select add #27
1798 atoms, 1661 bonds, 397 residues, 1 model selected
> view matrix models
> #27,-0.4262,0.53806,-0.72722,176.2,-0.24981,-0.84263,-0.47705,165.62,-0.86946,-0.021651,0.49354,102.24
> view matrix models
> #27,-0.4262,0.53806,-0.72722,178.78,-0.24981,-0.84263,-0.47705,174.86,-0.86946,-0.021651,0.49354,105.39
> view matrix models
> #27,-0.4262,0.53806,-0.72722,181.47,-0.24981,-0.84263,-0.47705,184.66,-0.86946,-0.021651,0.49354,109.78
> view matrix models
> #27,-0.4262,0.53806,-0.72722,190.87,-0.24981,-0.84263,-0.47705,217.94,-0.86946,-0.021651,0.49354,118.99
> view matrix models
> #27,-0.3858,0.47048,-0.7936,196.51,0.046117,-0.84929,-0.52592,214.13,-0.92143,-0.2395,0.30596,139.88
> view matrix models
> #27,-0.66587,0.4077,0.62482,112.13,-0.39323,0.51992,-0.75832,194.48,-0.63402,-0.75064,-0.18588,182.26
> view matrix models
> #27,-0.68529,0.37699,0.6231,113.74,-0.37744,0.54787,-0.74658,192.39,-0.62283,-0.74681,-0.23315,184.97
> view matrix models
> #27,-0.64501,-0.54498,0.53568,149.28,-0.48286,0.83399,0.26704,118.72,-0.59228,-0.086414,-0.80108,199.55
> view matrix models
> #27,-0.64501,-0.54498,0.53568,147.06,-0.48286,0.83399,0.26704,118.55,-0.59228,-0.086414,-0.80108,205.77
> view matrix models
> #27,-0.98854,-0.0066051,-0.15082,182.67,-0.13987,0.41609,0.8985,82.549,0.056821,0.9093,-0.41224,131.06
> view matrix models
> #27,-0.98854,-0.0066051,-0.15082,167.04,-0.13987,0.41609,0.8985,91.832,0.056821,0.9093,-0.41224,120.45
> view matrix models
> #27,-0.98854,-0.0066051,-0.15082,170.38,-0.13987,0.41609,0.8985,89.105,0.056821,0.9093,-0.41224,122.96
> view matrix models
> #27,-0.98854,-0.0066051,-0.15082,170.42,-0.13987,0.41609,0.8985,90.399,0.056821,0.9093,-0.41224,133.48
> volume #35 level 0.043
> open /Users/apple/Downloads/cryosparc_P371_J937_003_volume_map.mrc
Opened cryosparc_P371_J937_003_volume_map.mrc as #36, grid size 300,300,300,
pixel 0.867, shown at level 0.0245, step 2, values float32
> volume #36 level 0.06028
> hide #27 models
> select subtract #27
Nothing selected
> volume flip #36 axis z
Opened cryosparc_P371_J937_003_volume_map.mrc z flip as #37, grid size
300,300,300, pixel 0.867, shown at step 1, values float32
> transparency #37 50
> show #!31 models
> select add #31
2975 atoms, 2968 bonds, 437 residues, 1 model selected
> view matrix models
> #31,0.39135,-0.20933,0.89611,66.667,-0.16444,-0.97402,-0.15572,220.86,0.90543,-0.086415,-0.41561,82.36
> view matrix models
> #31,-0.095994,-0.17972,0.97902,91.144,-0.11035,-0.97558,-0.18991,219.49,0.98925,-0.12627,0.073818,51.003
> view matrix models
> #31,-0.095994,-0.17972,0.97902,86.989,-0.11035,-0.97558,-0.18991,196.02,0.98925,-0.12627,0.073818,43.81
> view matrix models
> #31,-0.14959,-0.29832,0.94267,99.755,-0.024842,-0.95196,-0.3052,195.83,0.98844,-0.069073,0.13499,36.818
> view matrix models
> #31,-0.14959,-0.29832,0.94267,100.18,-0.024842,-0.95196,-0.3052,202.18,0.98844,-0.069073,0.13499,38.064
> fitmap #31 inMap #37
Fit molecule copy of copy of copy of 1ezx (#31) to map
cryosparc_P371_J937_003_volume_map.mrc z flip (#37) using 2975 atoms
average map value = 0.08682, steps = 132
shifted from previous position = 2.02
rotated from previous position = 31.6 degrees
atoms outside contour = 867, contour level = 0.06028
Position of copy of copy of copy of 1ezx (#31) relative to
cryosparc_P371_J937_003_volume_map.mrc z flip (#37) coordinates:
Matrix rotation and translation
0.36233036 -0.11333577 0.92513335 57.46362679
-0.01935243 -0.99328021 -0.11410485 191.49517202
0.93184880 0.02344008 -0.36208890 68.00033796
Axis 0.82499051 -0.04027910 0.56370937
Axis point 0.00000000 96.54263836 19.29334389
Rotation angle (degrees) 175.21818737
Shift along axis 78.02612084
> mmaker #32 to #31
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 copy of copy of copy of 1ezx, chain A (#31) with copy of copy of
copy of 1ezx, chain A (#32), sequence alignment score = 1734
RMSD between 335 pruned atom pairs is 0.000 angstroms; (across all 335 pairs:
0.000)
> show #!32 models
> select subtract #31
Nothing selected
> hide #!32 models
> transparency #37 30
> transparency #37 65
> show #!32 models
> show #27 models
> mmaker #27 to #32
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 copy of copy of copy of 1ezx, chain C (#32) with 1oph, chain B
(#27), sequence alignment score = 997.3
RMSD between 122 pruned atom pairs is 0.798 angstroms; (across all 140 pairs:
2.232)
> hide #!32 models
> select #27/B: 195
5 atoms, 4 bonds, 1 residue, 1 model selected
> color sel red
> select add #27
1798 atoms, 1661 bonds, 397 residues, 1 model selected
> select subtract #27
Nothing selected
> select add #27
1798 atoms, 1661 bonds, 397 residues, 1 model selected
> view matrix models
> #27,0.0036574,-0.99591,-0.090234,167.1,0.079873,-0.089656,0.99276,103.86,-0.9968,-0.010838,0.079218,136.78
> view matrix models
> #27,0.0036574,-0.99591,-0.090234,167.32,0.079873,-0.089656,0.99276,103.5,-0.9968,-0.010838,0.079218,136.17
> view matrix models
> #27,0.0036574,-0.99591,-0.090234,167.31,0.079873,-0.089656,0.99276,103.59,-0.9968,-0.010838,0.079218,135.71
> view matrix models
> #27,-0.286,-0.74268,-0.6055,199.85,-0.56632,-0.37872,0.73202,146.21,-0.77297,0.55227,-0.31228,137.19
> view matrix models
> #27,-0.286,-0.74268,-0.6055,200.26,-0.56632,-0.37872,0.73202,145.27,-0.77297,0.55227,-0.31228,137.56
> view matrix models
> #27,-0.11735,-0.92157,-0.37006,186.61,-0.43047,-0.2886,0.85522,130.83,-0.89494,0.25966,-0.36284,153.64
> view matrix models
> #27,-0.11735,-0.92157,-0.37006,187.37,-0.43047,-0.2886,0.85522,129.56,-0.89494,0.25966,-0.36284,153.71
> fitmap #27 inMap #37
Fit molecule 1oph (#27) to map cryosparc_P371_J937_003_volume_map.mrc z flip
(#37) using 1798 atoms
average map value = 0.0548, steps = 128
shifted from previous position = 3.42
rotated from previous position = 38.8 degrees
atoms outside contour = 1047, contour level = 0.06028
Position of 1oph (#27) relative to cryosparc_P371_J937_003_volume_map.mrc z
flip (#37) coordinates:
Matrix rotation and translation
-0.45346895 -0.89029021 0.04182410 166.01007315
-0.59816316 0.33879139 0.72623772 117.01111106
-0.66073198 0.30430862 -0.68617018 166.01554475
Axis -0.48496079 0.80751043 0.33576770
Axis point 138.35331070 0.00000000 30.35915407
Rotation angle (degrees) 154.21383871
Shift along axis 69.72197468
> view matrix models
> #27,-0.92301,-0.085578,-0.37515,178.08,-0.38272,0.30509,0.87204,103.27,0.039826,0.94847,-0.31435,102.9
> view matrix models
> #27,-0.92301,-0.085578,-0.37515,178.04,-0.38272,0.30509,0.87204,107.02,0.039826,0.94847,-0.31435,104.53
> view matrix models
> #27,-0.8652,-0.36102,-0.348,184.03,-0.41726,0.13347,0.89893,111.83,-0.27809,0.92296,-0.26611,109.99
> view matrix models
> #27,-0.8652,-0.36102,-0.348,184.08,-0.41726,0.13347,0.89893,110,-0.27809,0.92296,-0.26611,108.82
> view matrix models
> #27,-0.74437,-0.58007,-0.33081,187.3,-0.42416,0.028093,0.90515,113.28,-0.51575,0.81408,-0.26695,118.33
> fitmap #27 inMap #37
Fit molecule 1oph (#27) to map cryosparc_P371_J937_003_volume_map.mrc z flip
(#37) using 1798 atoms
average map value = 0.05355, steps = 84
shifted from previous position = 0.767
rotated from previous position = 14.4 degrees
atoms outside contour = 1098, contour level = 0.06028
Position of 1oph (#27) relative to cryosparc_P371_J937_003_volume_map.mrc z
flip (#37) coordinates:
Matrix rotation and translation
-0.61577270 -0.75165872 -0.23629043 184.50519497
-0.34375795 -0.01355748 0.93896042 110.78003691
-0.70898128 0.65941290 -0.25004033 128.04401792
Axis -0.40864695 0.69098691 0.59627574
Axis point 135.45180710 0.00000000 -11.35956716
Rotation angle (degrees) 159.99876589
Shift along axis 77.49961288
> hide #!31 models
> close #34-37
> hide #27 models
> select subtract #27
Nothing selected
> save /Users/apple/Downloads/csparc.cxs includeMaps true
You deleted or moved a volume file that is still open in ChimeraX.
/Users/apple/Downloads/cryosparc_P371_J1081_noflex_map.mrc
To allow fast initial display of volume data ChimeraX does not read all data
from the file when it is first opened, and will later read more data when
needed. ChimeraX got an error trying to read the above file.
[Repeated 1 time(s)]
> close #29-30
> save /Users/apple/Downloads/csparc.cxs includeMaps true
——— End of log from Wed Dec 31 02:28:23 2025 ———
opened ChimeraX session
> open /Users/apple/Downloads/J1122.mrc
Opened J1122.mrc as #29, grid size 300,300,300, pixel 0.867, shown at level
0.0211, step 2, values float32
> volume #29 level 0.06448
> transparency #29 50
> show #!31 models
> hide #!31 models
> show #!32 models
> select add #32
3984 atoms, 3982 bonds, 5 pseudobonds, 592 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #32,-0.4387,-0.32363,-0.83834,223.29,0.093735,-0.94429,0.31548,159.1,-0.89373,0.059819,0.44459,173.61
> view matrix models
> #32,-0.051177,-0.06552,-0.99654,192.53,-0.071281,-0.99506,0.069084,187.1,-0.99614,0.074569,0.046254,202.65
> view matrix models
> #32,-0.051177,-0.06552,-0.99654,191.33,-0.071281,-0.99506,0.069084,184.14,-0.99614,0.074569,0.046254,203.41
> view matrix models
> #32,0.026039,-0.29812,-0.95417,195.35,0.13022,-0.94535,0.29892,154.62,-0.99114,-0.13204,0.014206,215.34
> view matrix models
> #32,0.026039,-0.29812,-0.95417,195.13,0.13022,-0.94535,0.29892,154.52,-0.99114,-0.13204,0.014206,218.61
> view matrix models
> #32,0.32421,-0.1599,-0.93237,166.33,0.029424,-0.98343,0.17889,170.24,-0.94553,-0.085432,-0.31413,231.84
> ui tool show "Fit in Map"
> fitmap #32 inMap #29
Fit molecule copy of copy of copy of 1ezx (#32) to map J1122.mrc (#29) using
3984 atoms
average map value = 0.08314, steps = 224
shifted from previous position = 4.3
rotated from previous position = 41.5 degrees
atoms outside contour = 1668, contour level = 0.06448
Position of copy of copy of copy of 1ezx (#32) relative to J1122.mrc (#29)
coordinates:
Matrix rotation and translation
-0.34900889 0.03003688 -0.93663792 206.58097603
0.14034902 -0.98653802 -0.08393380 177.23372304
-0.92655003 -0.16074986 0.34009489 197.98573410
Axis -0.56984891 -0.07483556 0.81833481
Axis point 168.52294892 102.29267921 0.00000000
Rotation angle (degrees) 176.13531334
Shift along axis 31.03528983
> volume #29 level 0.07099
> surface dust #29 size 8.67
> select subtract #32
Nothing selected
> open cryosparc_P371_J1130_component_001/J1130_component_001_frame_???.mrc
> vseries true
Opened map series J1130_component_001_frame_000.mrc as #30, 20 images, grid
size 300,300,300, pixel 0.867, shown at level 0.033, step 2, values float32
> volume #30.1 level 0.04835
> surface dust #29 size 8.67
> surface dust #30.1 size 8.67
> transparency #30 50
> volume #30.7 level 0.06047
> open /Users/apple/Downloads/J1134.mrc
Opened J1134.mrc as #34, grid size 300,300,300, pixel 0.867, shown at level
0.0252, step 2, values float32
> transparency #31 50
> volume #34 level 0.04544
> transparency #31450
Missing or invalid "percent" argument: Expected a number
> transparency #34 50
> hide #!32 models
> show #!34 models
> volume #34 level 0.05837
> hide #!30 models
> show #!30 models
> hide #!29 models
> show #!32 models
> show #!29 models
> hide #!34 models
> hide #!30 models
> show #!34 models
> hide #!29 models
> volume #34 level 0.0685
> mmaker #27 to #32
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 copy of copy of copy of 1ezx, chain C (#32) with 1oph, chain B
(#27), sequence alignment score = 997.3
RMSD between 122 pruned atom pairs is 0.798 angstroms; (across all 140 pairs:
2.232)
> show #27 models
> hide #!32 models
> hide #27 models
> show #!29 models
> hide #!34 models
> show #!23 models
> hide #!29 models
> show #!29 models
> show #27 models
> fitmap #27 inMap #29
Fit molecule 1oph (#27) to map J1122.mrc (#29) using 1798 atoms
average map value = 0.0518, steps = 144
shifted from previous position = 4.11
rotated from previous position = 22.4 degrees
atoms outside contour = 1430, contour level = 0.070992
Position of 1oph (#27) relative to J1122.mrc (#29) coordinates:
Matrix rotation and translation
0.02106068 0.97914469 -0.20206962 114.64292873
0.03717102 0.20120785 0.97884305 90.21390293
0.99908697 -0.02812623 -0.03215823 122.53280686
Axis -0.55065296 -0.65684271 -0.51511064
Axis point 6.14168786 0.00000000 32.08271580
Rotation angle (degrees) 113.88767131
Shift along axis -185.50276510
> select add #27
1798 atoms, 1661 bonds, 397 residues, 1 model selected
> mmaker #27 to #32
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 copy of copy of copy of 1ezx, chain C (#32) with 1oph, chain B
(#27), sequence alignment score = 997.3
RMSD between 122 pruned atom pairs is 0.798 angstroms; (across all 140 pairs:
2.232)
> view matrix models
> #27,-0.76366,-0.59209,0.2574,152.81,-0.32869,0.6997,0.63433,106.59,-0.55569,0.39981,-0.72895,190.1
> view matrix models
> #27,-0.76366,-0.59209,0.2574,153.88,-0.32869,0.6997,0.63433,107.32,-0.55569,0.39981,-0.72895,188.09
> view matrix models
> #27,-0.83313,-0.43989,0.33525,145.38,-0.083744,0.6995,0.70971,96.368,-0.54671,0.56321,-0.61961,175.22
> view matrix models
> #27,-0.74236,-0.59158,0.31452,149.59,-0.27194,0.69508,0.66552,104.03,-0.61232,0.40852,-0.67688,185.76
> view matrix models
> #27,-0.74236,-0.59158,0.31452,149.31,-0.27194,0.69508,0.66552,103.43,-0.61232,0.40852,-0.67688,186.03
> view matrix models
> #27,-0.74236,-0.59158,0.31452,149.1,-0.27194,0.69508,0.66552,103.48,-0.61232,0.40852,-0.67688,187.73
> view matrix models
> #27,-0.4433,-0.67999,0.58404,127,-0.43264,0.73295,0.52499,115.4,-0.78505,-0.019955,-0.61911,202.46
> view matrix models
> #27,-0.4433,-0.67999,0.58404,130.64,-0.43264,0.73295,0.52499,113.63,-0.78505,-0.019955,-0.61911,205.53
> fitmap #27 inMap #29
Fit molecule 1oph (#27) to map J1122.mrc (#29) using 1798 atoms
average map value = 0.05116, steps = 68
shifted from previous position = 2.69
rotated from previous position = 9.17 degrees
atoms outside contour = 1446, contour level = 0.070992
Position of 1oph (#27) relative to J1122.mrc (#29) coordinates:
Matrix rotation and translation
-0.36812181 -0.63861563 0.67576357 123.53211487
-0.32941202 0.76923775 0.54750435 107.83162875
-0.86946769 -0.02105634 -0.49354086 197.89559046
Axis -0.33937979 0.92236459 0.18456685
Axis point 134.62181234 0.00000000 42.50689250
Rotation angle (degrees) 123.10755810
Shift along axis 94.06073906
> view matrix models
> #27,0.36598,-0.2092,0.9068,76.029,-0.77877,0.46461,0.42149,137.29,-0.50949,-0.86045,0.0071194,184.16
> view matrix models
> #27,0.36598,-0.2092,0.9068,76.706,-0.77877,0.46461,0.42149,135.37,-0.50949,-0.86045,0.0071194,183.36
> fitmap #27 inMap #29
Fit molecule 1oph (#27) to map J1122.mrc (#29) using 1798 atoms
average map value = 0.05313, steps = 140
shifted from previous position = 4.46
rotated from previous position = 26.6 degrees
atoms outside contour = 1440, contour level = 0.070992
Position of 1oph (#27) relative to J1122.mrc (#29) coordinates:
Matrix rotation and translation
0.65758974 -0.02081924 0.75308850 73.16880294
-0.73687782 0.19027838 0.64869501 131.74587255
-0.15680180 -0.98150940 0.10978387 176.26543706
Axis -0.81528498 0.45504717 -0.35810958
Axis point 0.00000000 178.61895966 -24.20653672
Rotation angle (degrees) 91.21327181
Shift along axis -62.82518106
> show #!34 models
> hide #!29 models
> volume #34 level 0.07075
> close #30
> save /Users/apple/Downloads/csparc.cxs includeMaps true
——— End of log from Tue Jan 6 13:31:49 2026 ———
> view name session-start
opened ChimeraX session
> hide #!23 models
> select subtract #27
Nothing selected
> hide #27 models
> hide #!34 models
> show #!8 models
> view
> open 1oph fromDatabase pdb format mmcif
Summary of feedback from opening 1oph fetched from pdb
---
note | Fetching compressed mmCIF 1oph from http://files.rcsb.org/download/1oph.cif
1oph title:
Non-covalent complex between α-1-π-pittsburgh and S195A trypsin [more info...]
Chain information for 1oph #30
---
Chain | Description | UniProt
A | Alpha-1-antitrypsin precursor | A1AT_HUMAN 1-394
B | Trypsinogen, cationic precursor | TRY1_BOVIN -4-245
1oph mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| software_defined_assembly
> mmaker #30 to #8
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 1ezx, chain A (#8) with 1oph, chain A (#30), sequence alignment
score = 1610.1
RMSD between 212 pruned atom pairs is 0.928 angstroms; (across all 335 pairs:
9.705)
> hide #!8 models
> ui tool show "Show Sequence Viewer"
> sequence chain #30/A
Alignment identifier is 30/A
> select #30/A:21-22
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #30/A:21-83
484 atoms, 495 bonds, 63 residues, 1 model selected
> select #30/A:88
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #30/A:88-121
263 atoms, 267 bonds, 34 residues, 1 model selected
> select #30/A:121
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #30/A:105-121
127 atoms, 128 bonds, 17 residues, 1 model selected
> select #30/A:88
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #30/A:88-104
136 atoms, 138 bonds, 17 residues, 1 model selected
> select #30/A:21-45,88-104
341 atoms, 349 bonds, 42 residues, 1 model selected
> select #30/A:53
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #30/A:53-80
196 atoms, 198 bonds, 28 residues, 1 model selected
> select #30/A:21-45,53-80
401 atoms, 409 bonds, 53 residues, 1 model selected
> select #30/A:21-45,53-80,88-104
537 atoms, 547 bonds, 70 residues, 1 model selected
> select #30/A:21-45,53-80,88-104,127-137
622 atoms, 632 bonds, 81 residues, 1 model selected
> select #30/A:21-45,53-80,88-104,127-137,149-165
747 atoms, 757 bonds, 98 residues, 1 model selected
> select #30/A:21-45,53-80,88-104,127-137,149-165,199-203
783 atoms, 792 bonds, 103 residues, 1 model selected
> select #30/A:21-45,53-80,88-104,127-137,149-165,199-203,259-278
954 atoms, 965 bonds, 123 residues, 1 model selected
> select #30/A:21-45,53-80,88-104,127-137,149-165,199-203,259-278,299-306
1013 atoms, 1023 bonds, 131 residues, 1 model selected
> select
> #30/A:21-45,53-80,88-104,127-137,149-165,199-203,259-278,299-306,309-313
1053 atoms, 1063 bonds, 136 residues, 1 model selected
> select
> #30/A:21-45,53-80,88-104,127-137,149-165,199-203,259-278,299-306,309-313,349-353
1089 atoms, 1099 bonds, 141 residues, 1 model selected
> color sel hot pink
> color sel dim gray
> select clear
[Repeated 3 time(s)]
> select #30/A:112
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #30/A:112-121
71 atoms, 71 bonds, 10 residues, 1 model selected
> select #30/A:112-121,141-145
110 atoms, 110 bonds, 15 residues, 1 model selected
> select #30/A:112-121,141-145,182-191
200 atoms, 203 bonds, 25 residues, 1 model selected
> select #30/A:112-121,141-145,182-191,193-194
219 atoms, 223 bonds, 27 residues, 1 model selected
> select #30/A:112-121,141-145,182-191,193-194
219 atoms, 223 bonds, 27 residues, 1 model selected
> select #30/A:112-121,141-145,182-194
223 atoms, 228 bonds, 28 residues, 1 model selected
> select #30/A:112-121,141-145,182-194,204-211
294 atoms, 300 bonds, 36 residues, 1 model selected
> select #30/A:112-121,141-145,182-194,204-211,214
301 atoms, 306 bonds, 37 residues, 1 model selected
> select #30/A:112-121,141-145,182-194,204-211,214
301 atoms, 306 bonds, 37 residues, 1 model selected
> select #30/A:211
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #30/A:204-211
71 atoms, 72 bonds, 8 residues, 1 model selected
> select #30/A:214
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #30/A:214-232
152 atoms, 154 bonds, 19 residues, 1 model selected
> select #30/A:282
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #30/A:282-298
130 atoms, 132 bonds, 17 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #8/C #19/C #26/C #32/C
Alignment identifier is 1
> select add #30
4919 atoms, 4641 bonds, 975 residues, 1 model selected
> select subtract #30
Nothing selected
> select #30/A
3121 atoms, 2980 bonds, 578 residues, 1 model selected
> delete #30/A
> show #!8 models
> close #30
> open 1oph fromDatabase pdb format mmcif
1oph title:
Non-covalent complex between α-1-π-pittsburgh and S195A trypsin [more info...]
Chain information for 1oph #30
---
Chain | Description | UniProt
A | Alpha-1-antitrypsin precursor | A1AT_HUMAN 1-394
B | Trypsinogen, cationic precursor | TRY1_BOVIN -4-245
1oph mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| software_defined_assembly
> open 8pi2 fromDatabase pdb format mmcif
Summary of feedback from opening 8pi2 fetched from pdb
---
notes | Fetching compressed mmCIF 8pi2 from http://files.rcsb.org/download/8pi2.cif
Fetching CCD DMS from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/DMS/DMS.cif
Fetching CCD EDO from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/EDO/EDO.cif
8pi2 title:
Native alpha-1-antitrypsin at 1.5 Angstrom (Cys232Ser) [more info...]
Chain information for 8pi2 #35
---
Chain | Description | UniProt
A | Alpha-1-antitrypsin | A1AT_HUMAN 2-394
Non-standard residues in 8pi2 #35
---
DMS — dimethyl sulfoxide
EDO — 1,2-ethanediol (ethylene glycol)
GLY — glycine
203 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
2826 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> mmaker #30 to #8
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 1ezx, chain A (#8) with 1oph, chain A (#30), sequence alignment
score = 1610.1
RMSD between 212 pruned atom pairs is 0.928 angstroms; (across all 335 pairs:
9.705)
> mmaker #35 to #30
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 1oph, chain A (#30) with 8pi2, chain A (#35), sequence alignment
score = 1934.1
RMSD between 350 pruned atom pairs is 0.764 angstroms; (across all 371 pairs:
1.541)
> hide #!8 models
> hide #30 models
> show #30 models
> delete #30/A
> select add #35
5953 atoms, 5684 bonds, 699 residues, 1 model selected
> hide sel atoms
> select subtract #35
Nothing selected
> select helix
13863 atoms, 13950 bonds, 1635 residues, 21 models selected
> select add #30
15472 atoms, 15419 bonds, 2007 residues, 21 models selected
> select subtract #30
13674 atoms, 13758 bonds, 1610 residues, 20 models selected
> select add #31
15630 atoms, 15698 bonds, 1919 residues, 20 models selected
> select subtract #31
12655 atoms, 12730 bonds, 1482 residues, 19 models selected
> select add #32
15484 atoms, 15547 bonds, 5 pseudobonds, 1928 residues, 21 models selected
> select subtract #32
11500 atoms, 11565 bonds, 1336 residues, 18 models selected
> select add #33
14424 atoms, 14571 bonds, 2 pseudobonds, 1724 residues, 20 models selected
> select subtract #33
11234 atoms, 11301 bonds, 1302 residues, 17 models selected
> select add #35
15239 atoms, 15031 bonds, 1873 residues, 17 models selected
> select subtract #35
9286 atoms, 9347 bonds, 1174 residues, 16 models selected
> select add #27
10895 atoms, 10816 bonds, 1546 residues, 16 models selected
> select subtract #27
9097 atoms, 9155 bonds, 1149 residues, 15 models selected
> select add #26
11926 atoms, 11972 bonds, 5 pseudobonds, 1595 residues, 17 models selected
> select subtract #26
7942 atoms, 7990 bonds, 1003 residues, 14 models selected
> select add #25
9668 atoms, 9577 bonds, 1377 residues, 14 models selected
> select subtract #25
7785 atoms, 7832 bonds, 983 residues, 13 models selected
> select add #24
10709 atoms, 10838 bonds, 2 pseudobonds, 1371 residues, 15 models selected
> select subtract #24
7519 atoms, 7568 bonds, 949 residues, 12 models selected
> select add #23
9475 atoms, 9508 bonds, 1258 residues, 12 models selected
> select subtract #23
6500 atoms, 6540 bonds, 821 residues, 11 models selected
> select add #20
8226 atoms, 8127 bonds, 1195 residues, 11 models selected
> select subtract #20
6343 atoms, 6382 bonds, 801 residues, 10 models selected
> select add #19
9172 atoms, 9199 bonds, 5 pseudobonds, 1247 residues, 12 models selected
> select subtract #19
5188 atoms, 5217 bonds, 655 residues, 9 models selected
> select add #18
6914 atoms, 6804 bonds, 1029 residues, 9 models selected
> select subtract #18
5031 atoms, 5059 bonds, 635 residues, 8 models selected
> select add #17
7955 atoms, 8065 bonds, 2 pseudobonds, 1023 residues, 10 models selected
> select subtract #17
4765 atoms, 4795 bonds, 601 residues, 7 models selected
> select add #16
6721 atoms, 6735 bonds, 910 residues, 7 models selected
> select subtract #16
3746 atoms, 3767 bonds, 473 residues, 6 models selected
> select add #8
6575 atoms, 6584 bonds, 5 pseudobonds, 919 residues, 8 models selected
> select subtract #8
2591 atoms, 2602 bonds, 327 residues, 5 models selected
> select add #7
4317 atoms, 4189 bonds, 701 residues, 5 models selected
> select subtract #7
2434 atoms, 2444 bonds, 307 residues, 4 models selected
> select add #6
5358 atoms, 5450 bonds, 2 pseudobonds, 695 residues, 6 models selected
> select subtract #6
2168 atoms, 2180 bonds, 273 residues, 3 models selected
> select #35/A:340
19 atoms, 18 bonds, 1 residue, 1 model selected
Drag select of 11 residues
> select clear
> select #35/A:340
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #35/A:339
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #35/A:340
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #35/A:339
33 atoms, 31 bonds, 2 residues, 1 model selected
> select add #35/A:338
52 atoms, 49 bonds, 3 residues, 1 model selected
> select add #35/A:337
68 atoms, 64 bonds, 4 residues, 1 model selected
> select add #35/A:336
78 atoms, 73 bonds, 5 residues, 1 model selected
> select add #35/A:335
99 atoms, 93 bonds, 6 residues, 1 model selected
> select add #35/A:334
116 atoms, 110 bonds, 7 residues, 1 model selected
> select add #35/A:333
132 atoms, 125 bonds, 8 residues, 1 model selected
> select add #35/A:332
142 atoms, 134 bonds, 9 residues, 1 model selected
> select add #35/A:331
164 atoms, 155 bonds, 10 residues, 1 model selected
> select add #35/A:191
186 atoms, 176 bonds, 11 residues, 1 model selected
> select add #35/A:190
206 atoms, 196 bonds, 12 residues, 1 model selected
> select add #35/A:189
226 atoms, 216 bonds, 13 residues, 1 model selected
> select add #35/A:188
245 atoms, 234 bonds, 14 residues, 1 model selected
> select add #35/A:187
266 atoms, 255 bonds, 15 residues, 1 model selected
> select add #35/A:186
280 atoms, 268 bonds, 16 residues, 1 model selected
> select add #35/A:185
296 atoms, 283 bonds, 17 residues, 1 model selected
> select add #35/A:184
315 atoms, 301 bonds, 18 residues, 1 model selected
> select add #35/A:183
325 atoms, 310 bonds, 19 residues, 1 model selected
> select add #35/A:182
345 atoms, 330 bonds, 20 residues, 1 model selected
> select add #35/A:291
364 atoms, 348 bonds, 21 residues, 1 model selected
> select add #35/A:292
375 atoms, 358 bonds, 22 residues, 1 model selected
> select add #35/A:293
394 atoms, 376 bonds, 23 residues, 1 model selected
> select add #35/A:294
408 atoms, 389 bonds, 24 residues, 1 model selected
> select subtract #35/A:294
394 atoms, 376 bonds, 23 residues, 1 model selected
> select add #35/A:294
408 atoms, 389 bonds, 24 residues, 1 model selected
> select add #35/A:295
415 atoms, 395 bonds, 25 residues, 1 model selected
> select add #35/A:296
429 atoms, 408 bonds, 26 residues, 1 model selected
> select add #35/A:297
450 atoms, 429 bonds, 27 residues, 1 model selected
> select add #35/A:298
462 atoms, 440 bonds, 28 residues, 1 model selected
> select add #35/A:112
481 atoms, 458 bonds, 29 residues, 1 model selected
> select add #35/A:113
495 atoms, 471 bonds, 30 residues, 1 model selected
> select add #35/A:114
509 atoms, 484 bonds, 31 residues, 1 model selected
> select add #35/A:115
516 atoms, 490 bonds, 32 residues, 1 model selected
> select add #35/A:116
530 atoms, 503 bonds, 33 residues, 1 model selected
> select add #35/A:117
537 atoms, 509 bonds, 34 residues, 1 model selected
> select add #35/A:118
556 atoms, 527 bonds, 35 residues, 1 model selected
> select add #35/A:119
576 atoms, 547 bonds, 36 residues, 1 model selected
> select add #35/A:120
595 atoms, 565 bonds, 37 residues, 1 model selected
> select add #35/A:121
606 atoms, 575 bonds, 38 residues, 1 model selected
> select add #35/A:141
621 atoms, 589 bonds, 39 residues, 1 model selected
> select add #35/A:142
631 atoms, 598 bonds, 40 residues, 1 model selected
> select add #35/A:143
651 atoms, 618 bonds, 41 residues, 1 model selected
> select add #35/A:144
665 atoms, 631 bonds, 42 residues, 1 model selected
> select add #35/A:145
681 atoms, 646 bonds, 43 residues, 1 model selected
> color sel forest green
> color sel lime
> select clear
> select add #35/A:341
12 atoms, 11 bonds, 1 residue, 1 model selected
> select add #35/A:342
27 atoms, 25 bonds, 2 residues, 1 model selected
> select add #35/A:343
40 atoms, 37 bonds, 3 residues, 1 model selected
> select add #35/A:344
47 atoms, 43 bonds, 4 residues, 1 model selected
> select add #35/A:345
61 atoms, 56 bonds, 5 residues, 1 model selected
> select add #35/A:193
83 atoms, 77 bonds, 6 residues, 1 model selected
> select subtract #35/A:193
61 atoms, 56 bonds, 5 residues, 1 model selected
> select add #35/A:346
68 atoms, 62 bonds, 6 residues, 1 model selected
> select add #35/A:347
78 atoms, 71 bonds, 7 residues, 1 model selected
> select add #35/A:348
88 atoms, 80 bonds, 8 residues, 1 model selected
> select add #35/A:349
95 atoms, 86 bonds, 9 residues, 1 model selected
> select add #35/A:350
105 atoms, 95 bonds, 10 residues, 1 model selected
> select add #35/A:351
112 atoms, 101 bonds, 11 residues, 1 model selected
> select add #35/A:352
132 atoms, 121 bonds, 12 residues, 1 model selected
> select add #35/A:353
151 atoms, 139 bonds, 13 residues, 1 model selected
> select add #35/A:354
166 atoms, 153 bonds, 14 residues, 1 model selected
> select add #35/A:355
176 atoms, 162 bonds, 15 residues, 1 model selected
> select add #35/A:356
195 atoms, 180 bonds, 16 residues, 1 model selected
> select add #35/A:357
209 atoms, 194 bonds, 17 residues, 1 model selected
> select add #35/A:358
226 atoms, 210 bonds, 18 residues, 1 model selected
> select add #35/A:359
237 atoms, 220 bonds, 19 residues, 1 model selected
> select add #35/A:360
256 atoms, 238 bonds, 20 residues, 1 model selected
> select add #35/A:361
270 atoms, 252 bonds, 21 residues, 1 model selected
> select add #35/A:362
284 atoms, 266 bonds, 22 residues, 1 model selected
> select add #35/A:363
299 atoms, 280 bonds, 23 residues, 1 model selected
> select subtract #35/A:363
284 atoms, 266 bonds, 22 residues, 1 model selected
> color sel red
> select clear
> select add #35/A:363
15 atoms, 14 bonds, 1 residue, 1 model selected
> select add #35/A:364
31 atoms, 29 bonds, 2 residues, 1 model selected
> select add #35/A:365
53 atoms, 50 bonds, 3 residues, 1 model selected
> select add #35/A:282
77 atoms, 73 bonds, 4 residues, 1 model selected
> select add #35/A:283
88 atoms, 83 bonds, 5 residues, 1 model selected
> select add #35/A:284
98 atoms, 92 bonds, 6 residues, 1 model selected
> select add #35/A:285
109 atoms, 102 bonds, 7 residues, 1 model selected
> select add #35/A:286
128 atoms, 120 bonds, 8 residues, 1 model selected
> select add #35/A:287
146 atoms, 138 bonds, 9 residues, 1 model selected
> select add #35/A:288
165 atoms, 156 bonds, 10 residues, 1 model selected
> select add #35/A:289
179 atoms, 170 bonds, 11 residues, 1 model selected
> select add #35/A:224
198 atoms, 188 bonds, 12 residues, 1 model selected
> select add #35/A:223
222 atoms, 211 bonds, 13 residues, 1 model selected
> select add #35/A:222
244 atoms, 232 bonds, 14 residues, 1 model selected
> select add #35/A:221
261 atoms, 248 bonds, 15 residues, 1 model selected
> select add #35/A:220
278 atoms, 264 bonds, 16 residues, 1 model selected
> select add #35/A:219
292 atoms, 278 bonds, 17 residues, 1 model selected
> select add #35/A:218
308 atoms, 293 bonds, 18 residues, 1 model selected
> select add #35/A:217
330 atoms, 314 bonds, 19 residues, 1 model selected
> select add #35/A:216
346 atoms, 329 bonds, 20 residues, 1 model selected
> select add #35/A:215
360 atoms, 342 bonds, 21 residues, 1 model selected
> select add #35/A:214
374 atoms, 355 bonds, 22 residues, 1 model selected
> select add #35/A:204
389 atoms, 369 bonds, 23 residues, 1 model selected
> select add #35/A:205
404 atoms, 383 bonds, 24 residues, 1 model selected
> select add #35/A:206
419 atoms, 397 bonds, 25 residues, 1 model selected
> select subtract #35/A:206
404 atoms, 383 bonds, 24 residues, 1 model selected
> select add #35/A:207
416 atoms, 394 bonds, 25 residues, 1 model selected
> select add #35/A:206
431 atoms, 408 bonds, 26 residues, 1 model selected
> select add #35/A:208
451 atoms, 428 bonds, 27 residues, 1 model selected
> select add #35/A:209
468 atoms, 445 bonds, 28 residues, 1 model selected
> select add #35/A:210
484 atoms, 460 bonds, 29 residues, 1 model selected
> select add #35/A:211
496 atoms, 471 bonds, 30 residues, 1 model selected
> color sel light sea green
> color sel blue
> color sel cornflower blue
> select clear
> select add #35/A:228
14 atoms, 13 bonds, 1 residue, 1 model selected
> select add #35/A:229
33 atoms, 31 bonds, 2 residues, 1 model selected
> select add #35/A:230
50 atoms, 47 bonds, 3 residues, 1 model selected
> select add #35/A:231
67 atoms, 64 bonds, 4 residues, 1 model selected
> select add #35/A:232
78 atoms, 74 bonds, 5 residues, 1 model selected
> select add #35/A:237
89 atoms, 84 bonds, 6 residues, 1 model selected
> select add #35/A:238
113 atoms, 109 bonds, 7 residues, 1 model selected
> select add #35/A:239
129 atoms, 124 bonds, 8 residues, 1 model selected
> select add #35/A:240
148 atoms, 142 bonds, 9 residues, 1 model selected
> select add #35/A:241
167 atoms, 160 bonds, 10 residues, 1 model selected
> select add #35/A:242
184 atoms, 176 bonds, 11 residues, 1 model selected
> select add #35/A:243
200 atoms, 191 bonds, 12 residues, 1 model selected
> select add #35/A:244
221 atoms, 212 bonds, 13 residues, 1 model selected
> select add #35/A:248
231 atoms, 221 bonds, 14 residues, 1 model selected
> select add #35/A:249
245 atoms, 234 bonds, 15 residues, 1 model selected
> select add #35/A:250
255 atoms, 243 bonds, 16 residues, 1 model selected
> select add #35/A:251
274 atoms, 261 bonds, 17 residues, 1 model selected
> select add #35/A:252
294 atoms, 281 bonds, 18 residues, 1 model selected
> select add #35/A:253
314 atoms, 301 bonds, 19 residues, 1 model selected
> select add #35/A:254
333 atoms, 319 bonds, 20 residues, 1 model selected
> select add #35/A:255
347 atoms, 333 bonds, 21 residues, 1 model selected
> select add #35/A:247
361 atoms, 346 bonds, 22 residues, 1 model selected
> select add #35/A:246
368 atoms, 352 bonds, 23 residues, 1 model selected
> select add #35/A:245
387 atoms, 370 bonds, 24 residues, 1 model selected
> select add #35/A:376
402 atoms, 384 bonds, 25 residues, 1 model selected
> select add #35/A:375
421 atoms, 402 bonds, 26 residues, 1 model selected
> select add #35/A:374
438 atoms, 418 bonds, 27 residues, 1 model selected
> select add #35/A:373
457 atoms, 436 bonds, 28 residues, 1 model selected
> select add #35/A:372
477 atoms, 456 bonds, 29 residues, 1 model selected
> select add #35/A:371
493 atoms, 471 bonds, 30 residues, 1 model selected
> select add #35/A:370
513 atoms, 491 bonds, 31 residues, 1 model selected
> select add #35/A:388
529 atoms, 506 bonds, 32 residues, 1 model selected
> select add #35/A:387
551 atoms, 527 bonds, 33 residues, 1 model selected
> select add #35/A:386
558 atoms, 533 bonds, 34 residues, 1 model selected
> select add #35/A:385
575 atoms, 549 bonds, 35 residues, 1 model selected
> select add #35/A:384
595 atoms, 569 bonds, 36 residues, 1 model selected
> select add #35/A:383
614 atoms, 587 bonds, 37 residues, 1 model selected
> select add #35/A:382
628 atoms, 601 bonds, 38 residues, 1 model selected
> select add #35/A:50
647 atoms, 619 bonds, 39 residues, 1 model selected
> select add #35/A:51
667 atoms, 639 bonds, 40 residues, 1 model selected
> select add #35/A:52
687 atoms, 659 bonds, 41 residues, 1 model selected
> select add #35/A:227
707 atoms, 679 bonds, 42 residues, 1 model selected
> color sel yellow
> select clear
> select add #35/A:225
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel cornflower blue
> select clear
> select add #35/A:226
17 atoms, 16 bonds, 1 residue, 1 model selected
> color sel cornflower blue
> select clear
[Repeated 1 time(s)]
> select add #35/A:165
14 atoms, 13 bonds, 1 residue, 1 model selected
> select add #35/A:163
27 atoms, 25 bonds, 2 residues, 1 model selected
> select add #35/A:162
42 atoms, 39 bonds, 3 residues, 1 model selected
> select add #35/A:164
49 atoms, 45 bonds, 4 residues, 1 model selected
> select add #35/A:161
65 atoms, 60 bonds, 5 residues, 1 model selected
> select add #35/A:160
86 atoms, 81 bonds, 6 residues, 1 model selected
> select add #35/A:159
98 atoms, 92 bonds, 7 residues, 1 model selected
> select add #35/A:158
112 atoms, 105 bonds, 8 residues, 1 model selected
> select add #35/A:157
131 atoms, 123 bonds, 9 residues, 1 model selected
> select add #35/A:155
153 atoms, 144 bonds, 10 residues, 1 model selected
> select add #35/A:156
170 atoms, 160 bonds, 11 residues, 1 model selected
> select add #35/A:154
192 atoms, 181 bonds, 12 residues, 1 model selected
> select add #35/A:153
202 atoms, 190 bonds, 13 residues, 1 model selected
> select add #35/A:152
217 atoms, 204 bonds, 14 residues, 1 model selected
> select add #35/A:151
232 atoms, 218 bonds, 15 residues, 1 model selected
> select add #35/A:150
246 atoms, 231 bonds, 16 residues, 1 model selected
> select add #35/A:149
258 atoms, 242 bonds, 17 residues, 1 model selected
> select add #35/A:336
268 atoms, 251 bonds, 18 residues, 1 model selected
> select subtract #35/A:336
258 atoms, 242 bonds, 17 residues, 1 model selected
> select add #35/A:166
275 atoms, 258 bonds, 18 residues, 1 model selected
> select add #35/A:167
282 atoms, 264 bonds, 19 residues, 1 model selected
> select add #35/A:168
292 atoms, 273 bonds, 20 residues, 1 model selected
> select add #35/A:169
311 atoms, 291 bonds, 21 residues, 1 model selected
> select add #35/A:170
327 atoms, 306 bonds, 22 residues, 1 model selected
> select add #35/A:171
339 atoms, 317 bonds, 23 residues, 1 model selected
> select add #35/A:172
358 atoms, 335 bonds, 24 residues, 1 model selected
> select add #35/A:173
374 atoms, 350 bonds, 25 residues, 1 model selected
> select add #35/A:174
396 atoms, 371 bonds, 26 residues, 1 model selected
> select add #35/A:175
406 atoms, 380 bonds, 27 residues, 1 model selected
> select add #35/A:176
425 atoms, 398 bonds, 28 residues, 1 model selected
> select add #35/A:177
432 atoms, 404 bonds, 29 residues, 1 model selected
> select add #35/A:178
439 atoms, 410 bonds, 30 residues, 1 model selected
> select add #35/A:179
446 atoms, 416 bonds, 31 residues, 1 model selected
> select add #35/A:180
460 atoms, 429 bonds, 32 residues, 1 model selected
> select add #35/A:181
476 atoms, 444 bonds, 33 residues, 1 model selected
> select add #35
5953 atoms, 5684 bonds, 699 residues, 1 model selected
> select subtract #35
Nothing selected
> color #35 #bbb0abff
> color #35 #bbb8b6ff
> select add #35/A:340
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #35/A:339
33 atoms, 31 bonds, 2 residues, 1 model selected
> select add #35/A:338
52 atoms, 49 bonds, 3 residues, 1 model selected
> select add #35/A:337
68 atoms, 64 bonds, 4 residues, 1 model selected
> select add #35/A:336
78 atoms, 73 bonds, 5 residues, 1 model selected
> select add #35/A:335
99 atoms, 93 bonds, 6 residues, 1 model selected
> select add #35/A:334
116 atoms, 110 bonds, 7 residues, 1 model selected
> select add #35/A:333
132 atoms, 125 bonds, 8 residues, 1 model selected
> select add #35/A:332
142 atoms, 134 bonds, 9 residues, 1 model selected
> select add #35/A:331
164 atoms, 155 bonds, 10 residues, 1 model selected
> select add #35/A:291
183 atoms, 173 bonds, 11 residues, 1 model selected
> select add #35/A:292
194 atoms, 183 bonds, 12 residues, 1 model selected
> select add #35/A:293
213 atoms, 201 bonds, 13 residues, 1 model selected
> select add #35/A:294
227 atoms, 214 bonds, 14 residues, 1 model selected
> select add #35/A:295
234 atoms, 220 bonds, 15 residues, 1 model selected
> select add #35/A:296
248 atoms, 233 bonds, 16 residues, 1 model selected
> select add #35/A:297
269 atoms, 254 bonds, 17 residues, 1 model selected
> select add #35/A:298
281 atoms, 265 bonds, 18 residues, 1 model selected
> select add #35/A:191
303 atoms, 286 bonds, 19 residues, 1 model selected
> select add #35/A:190
323 atoms, 306 bonds, 20 residues, 1 model selected
> select add #35/A:189
343 atoms, 326 bonds, 21 residues, 1 model selected
> select add #35/A:188
362 atoms, 344 bonds, 22 residues, 1 model selected
> select add #35/A:187
383 atoms, 365 bonds, 23 residues, 1 model selected
> select add #35/A:186
397 atoms, 378 bonds, 24 residues, 1 model selected
> select add #35/A:185
413 atoms, 393 bonds, 25 residues, 1 model selected
> select add #35/A:184
432 atoms, 411 bonds, 26 residues, 1 model selected
> select add #35/A:183
442 atoms, 420 bonds, 27 residues, 1 model selected
> select add #35/A:182
462 atoms, 440 bonds, 28 residues, 1 model selected
> select add #35/A:121
473 atoms, 450 bonds, 29 residues, 1 model selected
> select add #35/A:120
492 atoms, 468 bonds, 30 residues, 1 model selected
> select add #35/A:119
512 atoms, 488 bonds, 31 residues, 1 model selected
> select add #35/A:118
531 atoms, 506 bonds, 32 residues, 1 model selected
> select add #35/A:117
538 atoms, 512 bonds, 33 residues, 1 model selected
> select add #35/A:116
552 atoms, 525 bonds, 34 residues, 1 model selected
> select add #35/A:115
559 atoms, 531 bonds, 35 residues, 1 model selected
> select add #35/A:114
573 atoms, 544 bonds, 36 residues, 1 model selected
> select add #35/A:113
587 atoms, 557 bonds, 37 residues, 1 model selected
> select add #35/A:112
606 atoms, 575 bonds, 38 residues, 1 model selected
> select add #35/A:141
621 atoms, 589 bonds, 39 residues, 1 model selected
> select add #35/A:142
631 atoms, 598 bonds, 40 residues, 1 model selected
> select add #35/A:143
651 atoms, 618 bonds, 41 residues, 1 model selected
> select add #35/A:144
665 atoms, 631 bonds, 42 residues, 1 model selected
> select add #35/A:145
681 atoms, 646 bonds, 43 residues, 1 model selected
> color sel light sea green
> color sel lime
> select clear
> select add #35/A:341
12 atoms, 11 bonds, 1 residue, 1 model selected
> select add #35/A:342
27 atoms, 25 bonds, 2 residues, 1 model selected
> select add #35/A:343
40 atoms, 37 bonds, 3 residues, 1 model selected
> select add #35/A:344
47 atoms, 43 bonds, 4 residues, 1 model selected
> select add #35/A:345
61 atoms, 56 bonds, 5 residues, 1 model selected
> select add #35/A:346
68 atoms, 62 bonds, 6 residues, 1 model selected
> select add #35/A:347
78 atoms, 71 bonds, 7 residues, 1 model selected
> select add #35/A:348
88 atoms, 80 bonds, 8 residues, 1 model selected
> select add #35/A:349
95 atoms, 86 bonds, 9 residues, 1 model selected
> select add #35/A:350
105 atoms, 95 bonds, 10 residues, 1 model selected
> select add #35/A:351
112 atoms, 101 bonds, 11 residues, 1 model selected
> select add #35/A:352
132 atoms, 121 bonds, 12 residues, 1 model selected
> select add #35/A:353
151 atoms, 139 bonds, 13 residues, 1 model selected
> select add #35/A:354
166 atoms, 153 bonds, 14 residues, 1 model selected
> select add #35/A:355
176 atoms, 162 bonds, 15 residues, 1 model selected
> select add #35/A:356
195 atoms, 180 bonds, 16 residues, 1 model selected
> select add #35/A:357
209 atoms, 194 bonds, 17 residues, 1 model selected
> select add #35/A:358
226 atoms, 210 bonds, 18 residues, 1 model selected
> select add #35/A:359
237 atoms, 220 bonds, 19 residues, 1 model selected
> select add #35/A:360
256 atoms, 238 bonds, 20 residues, 1 model selected
> select add #35/A:361
270 atoms, 252 bonds, 21 residues, 1 model selected
> select add #35/A:362
284 atoms, 266 bonds, 22 residues, 1 model selected
> color sel red
> select clear
> select add #35/A:165
14 atoms, 13 bonds, 1 residue, 1 model selected
> select add #35/A:164
21 atoms, 19 bonds, 2 residues, 1 model selected
> select add #35/A:163
34 atoms, 31 bonds, 3 residues, 1 model selected
> select add #35/A:162
49 atoms, 45 bonds, 4 residues, 1 model selected
> select add #35/A:161
65 atoms, 60 bonds, 5 residues, 1 model selected
> select add #35/A:160
86 atoms, 81 bonds, 6 residues, 1 model selected
> select add #35/A:159
98 atoms, 92 bonds, 7 residues, 1 model selected
> select add #35/A:158
112 atoms, 105 bonds, 8 residues, 1 model selected
> select add #35/A:157
131 atoms, 123 bonds, 9 residues, 1 model selected
> select add #35/A:156
148 atoms, 139 bonds, 10 residues, 1 model selected
> select add #35/A:155
170 atoms, 160 bonds, 11 residues, 1 model selected
> select add #35/A:154
192 atoms, 181 bonds, 12 residues, 1 model selected
> select add #35/A:153
202 atoms, 190 bonds, 13 residues, 1 model selected
> select add #35/A:152
217 atoms, 204 bonds, 14 residues, 1 model selected
> select add #35/A:151
232 atoms, 218 bonds, 15 residues, 1 model selected
> select add #35/A:150
246 atoms, 231 bonds, 16 residues, 1 model selected
> select add #35/A:149
258 atoms, 242 bonds, 17 residues, 1 model selected
> color sel magenta
> select clear
[Repeated 1 time(s)]
> color #30 #bcc7ceff
> color #30 #67c7ceff
> color #30 #0cc5ceff
> color #30 #07ce85ff
> color #30 #10ccceff
> color #30 #016fceff
> select #30/B:195
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> swapp S
Unknown command: swapp S
> delete #30/A swapaa S
Expected a keyword
> swapaa #30/B:195 ser
Using Dunbrack library
1oph #30/B ALA 195: phi -47.1, psi 140.5 trans
Density criteria with multiple volume models open;
Need to specify one to use via 'density' keyword.
> ui tool show Rotamers
Populating font family aliases took 55 ms. Replace uses of missing font family
"Times" with one that exists to avoid this cost.
> select #30/B:195
5 atoms, 4 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel SER rotLib Dunbrack
1oph #30/B ALA 195: phi -47.1, psi 140.5 trans
Changed 9 bond radii
No rotamers selected. Click the 'Calculate' button (not 'OK') to add a column
to the table.
> undo
[Repeated 2 time(s)]
> ui tool show Rotamers
> swapaa interactive sel SER rotLib Dunbrack
1oph #!30/B ALA 195: phi -47.1, psi 140.5 trans
Changed 9 bond radii
> swapaa #!30/B:195 SER criteria 3 rotLib Dunbrack
Using Dunbrack library
1oph #!30/B ALA 195: phi -47.1, psi 140.5 trans
Applying SER rotamer (chi angles: 64.0) to 1oph #!30/B SER 195
> hide sel atoms
[Repeated 2 time(s)]
> select #30/B:195
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #30/B:195
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> select clear
> select #30.1.1/A:1@CB
1 atom, 1 residue, 1 model selected
> swapaa #!30/B:195 SER criteria 2 rotLib Dunbrack
Using Dunbrack library
1oph #!30/B SER 195: phi -47.1, psi 140.5 trans
Applying SER rotamer (chi angles: -63.9) to 1oph #!30/B SER 195
> select #30/B:195
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> rainbow sel
> select clear
> select #35/A:358
17 atoms, 16 bonds, 1 residue, 1 model selected
> show sel atoms
> rainbow sel
[Repeated 1 time(s)]
> color sel byhetero
> color sel red
> color sel byhetero
> select clear
> open 1oph fromDatabase pdb format mmcif
1oph title:
Non-covalent complex between α-1-π-pittsburgh and S195A trypsin [more info...]
Chain information for 1oph #36
---
Chain | Description | UniProt
A | Alpha-1-antitrypsin precursor | A1AT_HUMAN 1-394
B | Trypsinogen, cationic precursor | TRY1_BOVIN -4-245
1oph mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| software_defined_assembly
> mmaker #36 to #35
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 8pi2, chain A (#35) with 1oph, chain A (#36), sequence alignment
score = 1934.1
RMSD between 350 pruned atom pairs is 0.764 angstroms; (across all 371 pairs:
1.541)
> select #36/A
3121 atoms, 2980 bonds, 578 residues, 1 model selected
> select #36/A: 358
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> hide #30 models
> show #30 models
> style sel stick
Changed 11 atom styles
> style sel ball
Changed 11 atom styles
> style sel stick
Changed 11 atom styles
> hide #35 models
> show #35 models
> select #36/A: 57
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #36
4919 atoms, 4641 bonds, 975 residues, 1 model selected
> select subtract #36
Nothing selected
> hide #36 models
> select #30/A: 57
Nothing selected
> select #30/B: 57
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select #30/B: 202
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #30/B: 102
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select #30/B: 194
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select add #30
1799 atoms, 1662 bonds, 397 residues, 1 model selected
> hide sel atoms
> select add #35
7752 atoms, 7346 bonds, 1096 residues, 2 models selected
> hide sel atoms
> select subtract #30
5953 atoms, 5684 bonds, 699 residues, 1 model selected
> select subtract #35
Nothing selected
> show #!8 models
> open 1ezx fromDatabase pdb format mmcif
Summary of feedback from opening 1ezx fetched from pdb
---
note | Fetching compressed mmCIF 1ezx from http://files.rcsb.org/download/1ezx.cif
1ezx title:
Crystal structure of A serpin:protease complex [more info...]
Chain information for 1ezx #37
---
Chain | Description | UniProt
A | ALPHA-1-ANTITRYPSIN | A1AT_HUMAN 24-358
B | ALPHA-1-ANTITRYPSIN | A1AT_HUMAN 359-394
C | TRYPSIN | TRY1_BOVIN 42-245
> mmaker #37 to #35
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 8pi2, chain A (#35) with 1ezx, chain A (#37), sequence alignment
score = 1629.2
RMSD between 219 pruned atom pairs is 0.866 angstroms; (across all 335 pairs:
9.271)
> hide #!8 models
> hide #30 models
> hide #35 models
> select #37/A
2686 atoms, 2674 bonds, 398 residues, 1 model selected
> select #37/A,B
2975 atoms, 2968 bonds, 437 residues, 1 model selected
> color sel dark gray
> select clear
> show #35 models
> hide #!37 models
> show #!37 models
> hide #35 models
> show #35 models
> hide #35 models
> select #37/C
1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 2 models selected
> show #30 models
> color (#!37 & sel) cornflower blue
> color (#!37 & sel) blue
> select clear
> select #37/C
1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 2 models selected
> color (#!37 & sel) cornflower blue
> select clear
> select #37/C
1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 2 models selected
> color (#!37 & sel) medium blue
> color (#!37 & sel) cornflower blue
> select 30
Expected an objects specifier or a keyword
> select 30/B
Expected an objects specifier or a keyword
> select 30/A
Expected an objects specifier or a keyword
> select #30
1799 atoms, 1662 bonds, 397 residues, 1 model selected
> color sel cornflower blue
> select clear
> select #37/A:291
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #37/A:292
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #37/A:291
14 atoms, 12 bonds, 2 residues, 1 model selected
> select add #37/A:293
22 atoms, 19 bonds, 3 residues, 1 model selected
> select add #37/A:294
29 atoms, 25 bonds, 4 residues, 1 model selected
> select add #37/A:295
33 atoms, 28 bonds, 5 residues, 1 model selected
> select add #37/A:296
40 atoms, 34 bonds, 6 residues, 1 model selected
> select add #37/A:297
52 atoms, 46 bonds, 7 residues, 1 model selected
> select add #37/A:298
60 atoms, 53 bonds, 8 residues, 1 model selected
> select add #37/A:340
68 atoms, 60 bonds, 9 residues, 1 model selected
> select add #37/A:339
75 atoms, 66 bonds, 10 residues, 1 model selected
> select add #37/A:338
83 atoms, 73 bonds, 11 residues, 1 model selected
> select add #37/A:337
90 atoms, 79 bonds, 12 residues, 1 model selected
> select add #37/A:336
95 atoms, 83 bonds, 13 residues, 1 model selected
> select add #37/A:335
104 atoms, 91 bonds, 14 residues, 1 model selected
> select add #37/A:334
114 atoms, 101 bonds, 15 residues, 1 model selected
> select add #37/A:333
121 atoms, 107 bonds, 16 residues, 1 model selected
> select add #37/A:332
126 atoms, 111 bonds, 17 residues, 1 model selected
> select add #37/A:331
135 atoms, 119 bonds, 18 residues, 1 model selected
> select add #37/A:330
141 atoms, 124 bonds, 19 residues, 1 model selected
> select add #37/A:329
149 atoms, 131 bonds, 20 residues, 1 model selected
> select add #37/A:328
158 atoms, 139 bonds, 21 residues, 1 model selected
> select add #37/A:327
166 atoms, 146 bonds, 22 residues, 1 model selected
> select add #37/A:357
173 atoms, 153 bonds, 23 residues, 1 model selected
> select add #37/A:356
181 atoms, 160 bonds, 24 residues, 1 model selected
> select add #37/A:355
186 atoms, 164 bonds, 25 residues, 1 model selected
> select add #37/A:354
195 atoms, 172 bonds, 26 residues, 1 model selected
> select add #37/A:353
203 atoms, 179 bonds, 27 residues, 1 model selected
> select add #37/A:352
214 atoms, 190 bonds, 28 residues, 1 model selected
> select add #37/A:351
222 atoms, 197 bonds, 29 residues, 1 model selected
> select add #37/A:350
227 atoms, 201 bonds, 30 residues, 1 model selected
> select add #37/A:349
231 atoms, 204 bonds, 31 residues, 1 model selected
> select add #37/A:348
236 atoms, 208 bonds, 32 residues, 1 model selected
> select add #37/A:347
241 atoms, 212 bonds, 33 residues, 1 model selected
> select add #37/A:346
250 atoms, 220 bonds, 34 residues, 1 model selected
> select add #37/A:345
257 atoms, 226 bonds, 35 residues, 1 model selected
> select add #37/A:344
261 atoms, 229 bonds, 36 residues, 1 model selected
> select add #37/A:193
270 atoms, 237 bonds, 37 residues, 1 model selected
> select add #37/A:192
274 atoms, 240 bonds, 38 residues, 1 model selected
> select add #37/A:191
283 atoms, 248 bonds, 39 residues, 1 model selected
> select add #37/A:190
294 atoms, 259 bonds, 40 residues, 1 model selected
> select add #37/A:189
305 atoms, 270 bonds, 41 residues, 1 model selected
> select add #37/A:188
313 atoms, 277 bonds, 42 residues, 1 model selected
> select add #37/A:187
325 atoms, 289 bonds, 43 residues, 1 model selected
> select add #37/A:186
333 atoms, 296 bonds, 44 residues, 1 model selected
> select add #37/A:185
340 atoms, 302 bonds, 45 residues, 1 model selected
> select add #37/A:184
348 atoms, 309 bonds, 46 residues, 1 model selected
> select add #37/A:183
353 atoms, 313 bonds, 47 residues, 1 model selected
> select add #37/A:182
364 atoms, 324 bonds, 48 residues, 1 model selected
> select subtract #37/A:182
353 atoms, 313 bonds, 47 residues, 1 model selected
> select subtract #37/A:183
348 atoms, 309 bonds, 46 residues, 1 model selected
> select subtract #37/A:184
340 atoms, 302 bonds, 45 residues, 1 model selected
> select subtract #37/A:185
333 atoms, 296 bonds, 44 residues, 1 model selected
> select subtract #37/A:186
325 atoms, 289 bonds, 43 residues, 1 model selected
> select subtract #37/A:187
313 atoms, 277 bonds, 42 residues, 1 model selected
> select subtract #37/A:188
305 atoms, 270 bonds, 41 residues, 1 model selected
> select subtract #37/A:189
294 atoms, 259 bonds, 40 residues, 1 model selected
> select subtract #37/A:190
283 atoms, 248 bonds, 39 residues, 1 model selected
> select subtract #37/A:191
274 atoms, 240 bonds, 38 residues, 1 model selected
> select subtract #37/A:192
270 atoms, 237 bonds, 37 residues, 1 model selected
> select subtract #37/A:193
261 atoms, 229 bonds, 36 residues, 1 model selected
> select subtract #37/A:357
254 atoms, 222 bonds, 35 residues, 1 model selected
> select subtract #37/A:356
246 atoms, 215 bonds, 34 residues, 1 model selected
> select subtract #37/A:355
241 atoms, 211 bonds, 33 residues, 1 model selected
> select subtract #37/A:354
232 atoms, 203 bonds, 32 residues, 1 model selected
> select subtract #37/A:353
224 atoms, 196 bonds, 31 residues, 1 model selected
> select subtract #37/A:352
213 atoms, 185 bonds, 30 residues, 1 model selected
> select subtract #37/A:351
205 atoms, 178 bonds, 29 residues, 1 model selected
> select subtract #37/A:350
200 atoms, 174 bonds, 28 residues, 1 model selected
> select subtract #37/A:349
196 atoms, 171 bonds, 27 residues, 1 model selected
> select subtract #37/A:348
191 atoms, 167 bonds, 26 residues, 1 model selected
> select subtract #37/A:347
186 atoms, 163 bonds, 25 residues, 1 model selected
> select subtract #37/A:346
177 atoms, 155 bonds, 24 residues, 1 model selected
> select subtract #37/A:345
170 atoms, 149 bonds, 23 residues, 1 model selected
> select subtract #37/A:344
166 atoms, 146 bonds, 22 residues, 1 model selected
> select add #37/A:193
175 atoms, 154 bonds, 23 residues, 1 model selected
> select add #37/A:192
179 atoms, 157 bonds, 24 residues, 1 model selected
> select add #37/A:191
188 atoms, 165 bonds, 25 residues, 1 model selected
> select add #37/A:190
199 atoms, 176 bonds, 26 residues, 1 model selected
> select add #37/A:189
210 atoms, 187 bonds, 27 residues, 1 model selected
> select add #37/A:188
218 atoms, 194 bonds, 28 residues, 1 model selected
> select add #37/A:187
230 atoms, 206 bonds, 29 residues, 1 model selected
> select add #37/A:186
238 atoms, 213 bonds, 30 residues, 1 model selected
> select add #37/A:185
245 atoms, 219 bonds, 31 residues, 1 model selected
> select add #37/A:184
253 atoms, 226 bonds, 32 residues, 1 model selected
> select add #37/A:183
258 atoms, 230 bonds, 33 residues, 1 model selected
> select add #37/A:182
269 atoms, 241 bonds, 34 residues, 1 model selected
> select add #37/A:111
278 atoms, 249 bonds, 35 residues, 1 model selected
> select add #37/A:112
286 atoms, 256 bonds, 36 residues, 1 model selected
> select subtract #37/A:112
278 atoms, 249 bonds, 35 residues, 1 model selected
> select add #37/A:112
286 atoms, 256 bonds, 36 residues, 1 model selected
> select add #37/A:113
293 atoms, 262 bonds, 37 residues, 1 model selected
> select add #37/A:114
300 atoms, 268 bonds, 38 residues, 1 model selected
> select add #37/A:115
304 atoms, 271 bonds, 39 residues, 1 model selected
> select add #37/A:116
312 atoms, 278 bonds, 40 residues, 1 model selected
> select add #37/A:117
316 atoms, 281 bonds, 41 residues, 1 model selected
> select add #37/A:118
324 atoms, 288 bonds, 42 residues, 1 model selected
> select subtract #37/A:118
316 atoms, 281 bonds, 41 residues, 1 model selected
> select add #37/A:119
327 atoms, 292 bonds, 42 residues, 1 model selected
> select add #37/A:118
335 atoms, 299 bonds, 43 residues, 1 model selected
> select add #37/A:120
343 atoms, 306 bonds, 44 residues, 1 model selected
> select add #37/A:121
349 atoms, 311 bonds, 45 residues, 1 model selected
> select add #37/A:145
356 atoms, 317 bonds, 46 residues, 1 model selected
> select add #37/A:144
363 atoms, 323 bonds, 47 residues, 1 model selected
> select add #37/A:143
374 atoms, 334 bonds, 48 residues, 1 model selected
> select add #37/A:142
379 atoms, 338 bonds, 49 residues, 1 model selected
> select add #37/A:141
388 atoms, 346 bonds, 50 residues, 1 model selected
> color sel cyan
> color sel forest green
> color sel lime
> select clear
> select add #37/A:358
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #37/A:357
15 atoms, 14 bonds, 2 residues, 1 model selected
> select add #37/A:356
23 atoms, 21 bonds, 3 residues, 1 model selected
> select add #37/A:355
28 atoms, 25 bonds, 4 residues, 1 model selected
> select add #37/A:354
37 atoms, 33 bonds, 5 residues, 1 model selected
> select add #37/A:353
45 atoms, 40 bonds, 6 residues, 1 model selected
> select add #37/A:352
56 atoms, 51 bonds, 7 residues, 1 model selected
> select add #37/A:351
64 atoms, 58 bonds, 8 residues, 1 model selected
> select add #37/A:350
69 atoms, 62 bonds, 9 residues, 1 model selected
> select add #37/A:349
73 atoms, 65 bonds, 10 residues, 1 model selected
> select add #37/A:348
78 atoms, 69 bonds, 11 residues, 1 model selected
> select add #37/A:347
83 atoms, 73 bonds, 12 residues, 1 model selected
> select add #37/A:346
92 atoms, 81 bonds, 13 residues, 1 model selected
> select add #37/A:345
99 atoms, 87 bonds, 14 residues, 1 model selected
> select add #37/A:344
103 atoms, 90 bonds, 15 residues, 1 model selected
> select add #37/A:341
111 atoms, 97 bonds, 16 residues, 1 model selected
> select add #37/A:342
120 atoms, 105 bonds, 17 residues, 1 model selected
> select add #37/A:343
129 atoms, 113 bonds, 18 residues, 1 model selected
> color sel red
> select clear
> hide #30 models
> show #30 models
> hide #30 models
> hide #!37 models
> show #!37 models
> select add #37
3984 atoms, 3982 bonds, 5 pseudobonds, 592 residues, 3 models selected
> select clear
[Repeated 2 time(s)]
> hide #37.1.1 models
> select #37/C: 195
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
[Repeated 1 time(s)]
> show #35 models
> hide #35 models
> select add #37/A:165
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #37/A:164
11 atoms, 9 bonds, 2 residues, 1 model selected
> select add #37/A:163
16 atoms, 13 bonds, 3 residues, 1 model selected
> select add #37/A:162
25 atoms, 21 bonds, 4 residues, 1 model selected
> select add #37/A:161
32 atoms, 27 bonds, 5 residues, 1 model selected
> select add #37/A:159
40 atoms, 34 bonds, 6 residues, 1 model selected
> select add #37/A:158
48 atoms, 41 bonds, 7 residues, 1 model selected
> select add #37/A:160
60 atoms, 53 bonds, 8 residues, 1 model selected
> select add #37/A:157
68 atoms, 60 bonds, 9 residues, 1 model selected
> select add #37/A:156
77 atoms, 68 bonds, 10 residues, 1 model selected
> select add #37/A:155
83 atoms, 73 bonds, 11 residues, 1 model selected
> select add #37/A:154
92 atoms, 81 bonds, 12 residues, 1 model selected
> select add #37/A:153
97 atoms, 85 bonds, 13 residues, 1 model selected
> select add #37/A:152
102 atoms, 89 bonds, 14 residues, 1 model selected
> select add #37/A:151
111 atoms, 97 bonds, 15 residues, 1 model selected
> select add #37/A:150
118 atoms, 103 bonds, 16 residues, 1 model selected
> select add #37/A:149
126 atoms, 110 bonds, 17 residues, 1 model selected
> color sel magenta
> select clear
> show #35 models
> show #30 models
> hide #!37 models
> select #30/B: 195
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> save "/Users/amy/Desktop/3C11_Fab_AAT_NE/make pictures/1oph_michaelis
> complex.jpg" width 935 height 668 supersample 3
> ui tool show Toolbar
> save /Users/amy/Desktop/image1.png supersample 3
> save "/Users/amy/Desktop/3C11_Fab_AAT_NE/make pictures/1oph_michaelis
> complex.png" width 935 height 668 supersample 3 transparentBackground true
> show #!37 models
> hide #30 models
> hide #35 models
> undo
> hide #35 models
> view
> hide #!37 models
> show #35 models
> show #!37 models
> hide #!37 models
> show #30 models
> save "/Users/amy/Desktop/3C11_Fab_AAT_NE/make pictures/1oph_michaelis
> complex.png" width 935 height 668 supersample 3 transparentBackground true
> hide #30 models
> hide #35 models
> show #!37 models
> save "/Users/amy/Desktop/3C11_Fab_AAT_NE/make pictures/1ezx_final
> complex.png" width 935 height 668 supersample 3 transparentBackground true
> save /Users/amy/Desktop/3C11_Fab_AAT_NE/csparc.cxs includeMaps true
——— End of log from Sun Feb 1 23:24:08 2026 ———
> view name session-start
opened ChimeraX session
> open 9hud fromDatabase pdb format mmcif
9hud title:
Alpha-1-antitrypsin in the cleaved conformation in complex with a
conformationally nonselective Fab fragment [more info...]
Chain information for 9hud #38
---
Chain | Description | UniProt
A C | Alpha-1-antitrypsin | A1AT_HUMAN 2-354
B D | Short peptide from AAT | A1AT_HUMAN 355-394
H I | FAB 9C5 heavy chain |
L M | FAB 9C5 light chain |
Non-standard residues in 9hud #38
---
CL — chloride ion
EDO — 1,2-ethanediol (ethylene glycol)
GLY — glycine
GOL — glycerol (glycerin; propane-1,2,3-triol)
LYS — lysine
NA — sodium ion
9hud mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
61 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
12039 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> hide #!37-38 cartoons
> show #!37-38 cartoons
> hide #!37-38 atoms
> select #38/A
2567 atoms, 2550 bonds, 398 residues, 1 model selected
> select #38/B
252 atoms, 251 bonds, 40 residues, 1 model selected
> select #38/C
2612 atoms, 2578 bonds, 415 residues, 1 model selected
> select #38/C,D
2873 atoms, 2840 bonds, 454 residues, 1 model selected
> delete #38/C,D
> select #38/H
1713 atoms, 1651 bonds, 322 residues, 1 model selected
> select #38/I
1736 atoms, 1654 bonds, 1 pseudobond, 338 residues, 2 models selected
> delete #38/I
> select #38/M
1766 atoms, 1691 bonds, 328 residues, 1 model selected
> delete #38/M
> hide #!37 models
> show #!37 models
> mmaker #38 to #37
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 1ezx, chain A (#37) with 9hud, chain A (#38), sequence alignment
score = 1674.4
RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
0.519)
> save /Users/amy/Desktop/3C11_Fab_AAT_NE/csparc.cxs includeMaps true
——— End of log from Wed Feb 11 13:24:40 2026 ———
> view name session-start
opened ChimeraX session
> open /Users/amy/Downloads/cryosparc_P483_J66_004_volume_map.mrc
Opened cryosparc_P483_J66_004_volume_map.mrc as #39, grid size 400,400,400,
pixel 0.723, shown at level 0.00725, step 2, values float32
> volume #39 level 0.0301
> hide #!37 models
> hide #!38 models
> volume #39 level 0.08437
> open /Users/amy/Downloads/cryosparc_P483_J69_005_volume_map.mrc
Opened cryosparc_P483_J69_005_volume_map.mrc as #40, grid size 400,400,400,
pixel 0.723, shown at level 0.00425, step 2, values float32
> volume #40 level 0.02603
> volume #40 level 0.05112
> transparency #40 50
> show #!39 models
> hide #!39 models
> show #!38 models
> select add #38
6282 atoms, 6138 bonds, 1077 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #38,-0.23813,0.96316,-0.12499,103.01,0.23278,-0.068345,-0.97012,107.01,-0.94292,-0.26011,-0.20793,320.16
> view matrix models
> #38,-0.35239,0.53131,-0.77041,145.72,-0.23758,-0.84704,-0.47549,205.11,-0.90519,0.015476,0.42472,295.71
> view matrix models
> #38,0.095516,0.64963,-0.75423,70.134,0.59254,-0.64594,-0.48131,66.164,-0.79986,-0.40094,-0.44663,305.92
> view matrix models
> #38,0.23814,0.79731,-0.5546,39.413,0.91725,-0.37235,-0.14145,0.058888,-0.31929,-0.47502,-0.82,237.42
> view matrix models
> #38,-0.29619,0.8953,-0.33273,117.39,0.7752,0.42884,0.46386,-15.784,0.55798,-0.12055,-0.82105,85.078
> view matrix models
> #38,-0.30596,0.51089,-0.80335,139.57,0.54659,0.78515,0.29115,8.8601,0.7795,-0.35003,-0.51948,55.076
> view matrix models
> #38,-0.30596,0.51089,-0.80335,160.4,0.54659,0.78515,0.29115,-4.0241,0.7795,-0.35003,-0.51948,56.001
> view matrix models
> #38,0.2554,0.95891,-0.12357,45.918,0.33368,0.032535,0.94213,50.395,0.90743,-0.28185,-0.31165,30.553
> view matrix models
> #38,0.28907,0.71313,0.63866,40.495,-0.045867,-0.65606,0.75332,139.21,0.95621,-0.24706,-0.15694,19.569
> view matrix models
> #38,0.66315,0.74847,0.0052223,-12.11,0.30094,-0.27301,0.91373,67.652,0.68532,-0.60437,-0.40629,79.243
> view matrix models
> #38,0.66315,0.74847,0.0052223,-14.717,0.30094,-0.27301,0.91373,95.231,0.68532,-0.60437,-0.40629,75.309
> view matrix models
> #38,0.66315,0.74847,0.0052223,9.7058,0.30094,-0.27301,0.91373,102.14,0.68532,-0.60437,-0.40629,70.114
> ui tool show "Fit in Map"
> fitmap #38 inMap #40
Fit molecule 9hud (#38) to map cryosparc_P483_J69_005_volume_map.mrc (#40)
using 6282 atoms
average map value = 0.0417, steps = 128
shifted from previous position = 4.51
rotated from previous position = 8.35 degrees
atoms outside contour = 4033, contour level = 0.051121
Position of 9hud (#38) relative to cryosparc_P483_J69_005_volume_map.mrc (#40)
coordinates:
Matrix rotation and translation
0.65684785 0.74878514 0.08872268 11.05139992
0.33454956 -0.39485965 0.85566491 105.25041377
0.67574218 -0.53235953 -0.50986845 72.64892317
Axis -0.88808312 -0.37558568 -0.26503541
Axis point 0.00000000 65.04529101 13.14028850
Rotation angle (degrees) 128.60443789
Shift along axis -68.59964747
> select subtract #38
Nothing selected
> volume #40 level 0.0597
> hide #!40 models
> show #!40 models
> hide #!38 models
> show #!38 models
> hide #!40 models
> show #!40 models
> hide #!38 models
> show #!38 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!38 models
> volume flip #40 axis z
Opened cryosparc_P483_J69_005_volume_map.mrc z flip as #41, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> show #!38 models
> select add #38
6282 atoms, 6138 bonds, 1077 residues, 1 model selected
> view matrix models
> #38,0.65685,0.74879,0.088723,12.679,0.33455,-0.39486,0.85566,109.56,0.67574,-0.53236,-0.50987,57.685
> view matrix models
> #38,-0.58254,0.54788,0.6004,210.02,0.59834,-0.2109,0.77299,61.815,0.55013,0.80954,-0.20496,22.25
> view matrix models
> #38,-0.40435,-0.85962,0.31233,239.45,0.49216,0.083334,0.86651,66.149,-0.7709,0.50409,0.38937,235.48
> view matrix models
> #38,-0.56895,-0.81456,0.11308,266.25,0.44686,-0.19079,0.87402,83.739,-0.69037,0.54781,0.47254,220.03
> view matrix models
> #38,-0.56895,-0.81456,0.11308,265.73,0.44686,-0.19079,0.87402,80.959,-0.69037,0.54781,0.47254,214.99
> fitmap #38 inMap #41
Fit molecule 9hud (#38) to map cryosparc_P483_J69_005_volume_map.mrc z flip
(#41) using 6282 atoms
average map value = 0.05473, steps = 216
shifted from previous position = 2.37
rotated from previous position = 33 degrees
atoms outside contour = 3800, contour level = 0.059703
Position of 9hud (#38) relative to cryosparc_P483_J69_005_volume_map.mrc z
flip (#41) coordinates:
Matrix rotation and translation
-0.75082147 -0.55505166 -0.35802903 289.09205452
0.04746292 -0.58599102 0.80892632 158.98706928
-0.65879769 0.59036614 0.46631901 208.65076835
Axis -0.30870385 0.42481867 0.85101765
Axis point 172.41915491 63.65569402 0.00000000
Rotation angle (degrees) 159.26804372
Shift along axis 155.86233044
> select subtract #38
Nothing selected
> volume #41 level 0.05159
> select add #38
6282 atoms, 6138 bonds, 1077 residues, 1 model selected
> view matrix models
> #38,-0.75082,-0.55505,-0.35803,289.14,0.047463,-0.58599,0.80893,158.79,-0.6588,0.59037,0.46632,207.97
> view matrix models
> #38,-0.75082,-0.55505,-0.35803,289.16,0.047463,-0.58599,0.80893,157.96,-0.6588,0.59037,0.46632,207.03
> view matrix models
> #38,-0.75082,-0.55505,-0.35803,288.72,0.047463,-0.58599,0.80893,155.88,-0.6588,0.59037,0.46632,205.57
> fitmap #38 inMap #41
Fit molecule 9hud (#38) to map cryosparc_P483_J69_005_volume_map.mrc z flip
(#41) using 6282 atoms
average map value = 0.05473, steps = 72
shifted from previous position = 4.4
rotated from previous position = 0.101 degrees
atoms outside contour = 3342, contour level = 0.051588
Position of 9hud (#38) relative to cryosparc_P483_J69_005_volume_map.mrc z
flip (#41) coordinates:
Matrix rotation and translation
-0.75090265 -0.55404999 -0.35940760 289.07011046
0.04645479 -0.58718152 0.80812117 159.19876899
-0.65877702 0.59012412 0.46665444 208.66676414
Axis -0.30899016 0.42432779 0.85115863
Axis point 172.44704823 63.68649423 0.00000000
Rotation angle (degrees) 159.34394496
Shift along axis 155.84115924
> view matrix models
> #38,-0.7509,-0.55405,-0.35941,287.93,0.046455,-0.58718,0.80812,155.5,-0.65878,0.59012,0.46665,206.09
> fitmap #38 inMap #41
Fit molecule 9hud (#38) to map cryosparc_P483_J69_005_volume_map.mrc z flip
(#41) using 6282 atoms
average map value = 0.05473, steps = 92
shifted from previous position = 4.65
rotated from previous position = 0.00364 degrees
atoms outside contour = 3341, contour level = 0.051588
Position of 9hud (#38) relative to cryosparc_P483_J69_005_volume_map.mrc z
flip (#41) coordinates:
Matrix rotation and translation
-0.75086696 -0.55406598 -0.35945751 289.07124867
0.04643032 -0.58719553 0.80811239 159.20847697
-0.65881943 0.59009517 0.46663119 208.66191835
Axis -0.30902059 0.42431965 0.85115164
Axis point 172.44904391 63.69342969 0.00000000
Rotation angle (degrees) 159.34407294
Shift along axis 155.82925281
> select subtract #38
Nothing selected
> combine #38 close false
> hide #!38 models
> select #42/A
2567 atoms, 2550 bonds, 398 residues, 1 model selected
> select #42/M
Nothing selected
> select #42/M
Nothing selected
> select #42/I
Nothing selected
> select #42/H
1713 atoms, 1651 bonds, 322 residues, 1 model selected
> delete #42/H
> select #42/N
Nothing selected
> select #42/I
Nothing selected
> select #42/L
1750 atoms, 1686 bonds, 317 residues, 1 model selected
> delete #42/L
> fitmap #42 inMap #41
Fit molecule copy of 9hud (#42) to map cryosparc_P483_J69_005_volume_map.mrc z
flip (#41) using 2819 atoms
average map value = 0.06533, steps = 56
shifted from previous position = 0.821
rotated from previous position = 3.38 degrees
atoms outside contour = 1262, contour level = 0.051588
Position of copy of 9hud (#42) relative to
cryosparc_P483_J69_005_volume_map.mrc z flip (#41) coordinates:
Matrix rotation and translation
-0.73693347 -0.57914780 -0.34859273 288.27078922
0.03048667 -0.54364745 0.83875981 157.64342584
-0.67527744 0.60748274 0.41828829 210.31462354
Axis -0.31712566 0.44794803 0.83592696
Axis point 174.06638485 60.58096428 0.00000000
Rotation angle (degrees) 158.61421520
Shift along axis 155.00566094
> volume #41 level 0.06516
> select add #42
2819 atoms, 2801 bonds, 438 residues, 1 model selected
> view matrix models
> #42,-0.73693,-0.57915,-0.34859,287.85,0.030487,-0.54365,0.83876,156.54,-0.67528,0.60748,0.41829,208.51
> fitmap #42 inMap #41
Fit molecule copy of 9hud (#42) to map cryosparc_P483_J69_005_volume_map.mrc z
flip (#41) using 2819 atoms
average map value = 0.06533, steps = 76
shifted from previous position = 2.15
rotated from previous position = 0.0105 degrees
atoms outside contour = 1566, contour level = 0.065161
Position of copy of 9hud (#42) relative to
cryosparc_P483_J69_005_volume_map.mrc z flip (#41) coordinates:
Matrix rotation and translation
-0.73689140 -0.57919551 -0.34860239 288.27541199
0.03038436 -0.54353165 0.83883856 157.64897324
-0.67532796 0.60754087 0.41812229 210.31189981
Axis -0.31716299 0.44801683 0.83587592
Axis point 174.07498439 60.57428048 0.00000000
Rotation angle (degrees) 158.61485484
Shift along axis 154.99375355
> view matrix models
> #42,-0.73689,-0.5792,-0.3486,286.89,0.030384,-0.54353,0.83884,156.41,-0.67533,0.60754,0.41812,208.9
> view matrix models
> #42,-0.73689,-0.5792,-0.3486,287.57,0.030384,-0.54353,0.83884,158.73,-0.67533,0.60754,0.41812,212.26
> view matrix models
> #42,-0.73689,-0.5792,-0.3486,287.63,0.030384,-0.54353,0.83884,158.66,-0.67533,0.60754,0.41812,212.24
> fitmap #42 inMap #41
Fit molecule copy of 9hud (#42) to map cryosparc_P483_J69_005_volume_map.mrc z
flip (#41) using 2819 atoms
average map value = 0.06533, steps = 76
shifted from previous position = 2.27
rotated from previous position = 0.0141 degrees
atoms outside contour = 1565, contour level = 0.065161
Position of copy of 9hud (#42) relative to
cryosparc_P483_J69_005_volume_map.mrc z flip (#41) coordinates:
Matrix rotation and translation
-0.73682803 -0.57935101 -0.34847792 288.27467210
0.03043622 -0.54334125 0.83896003 157.62886136
-0.67539477 0.60756292 0.41798231 210.32004980
Axis -0.31717295 0.44810058 0.83582725
Axis point 174.07853761 60.56677345 0.00000000
Rotation angle (degrees) 158.60591524
Shift along axis 154.99188631
> select subtract #42
Nothing selected
> show #!38 models
> mmaker #38 to #42
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 copy of 9hud, chain A (#42) with 9hud, chain A (#38), sequence
alignment score = 1849.2
RMSD between 332 pruned atom pairs is 0.000 angstroms; (across all 332 pairs:
0.000)
> hide #!42 models
> hide #!38 models
> show #!38 models
> show #!37 models
> mmaker #37 to #38
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 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
score = 1674.4
RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
0.519)
> open /Users/amy/Downloads/cryosparc_P483_J81_008_volume_map.mrc
Opened cryosparc_P483_J81_008_volume_map.mrc as #43, grid size 400,400,400,
pixel 0.723, shown at level 0.00732, step 2, values float32
> hide #!37 models
> hide #!38 models
> hide #!41 models
> surface dust #43 size 7.23
> volume #43 level 0.06119
> volume #43 level 0.0273
> volume flip #43 axis z
Opened cryosparc_P483_J81_008_volume_map.mrc z flip as #44, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> transparency #44 50
> volume #44 level 0.03941
> volume #44 level 0.04042
> open /Users/amy/Downloads/cryosparc_P483_J66_004_volume_map.mrc
Opened cryosparc_P483_J66_004_volume_map.mrc as #45, grid size 400,400,400,
pixel 0.723, shown at level 0.00725, step 2, values float32
> volume #45 level 0.06094
> open /Users/amy/Downloads/cryosparc_P483_J72_006_volume_map.mrc
Opened cryosparc_P483_J72_006_volume_map.mrc as #46, grid size 400,400,400,
pixel 0.723, shown at level 0.0048, step 2, values float32
> volume #46 level 0.04807
> transparency #46 50
> show #!42 models
> hide #!42 models
> show #!38 models
> select add #38
6282 atoms, 6138 bonds, 1077 residues, 1 model selected
> view matrix models
> #38,-0.73683,-0.57935,-0.34848,292.33,0.030436,-0.54334,0.83896,164.74,-0.67539,0.60756,0.41798,237.37
> view matrix models
> #38,-0.38309,-0.69929,0.60352,229.08,0.62032,0.28936,0.72902,40.857,-0.68443,0.65365,0.32294,238.22
> view matrix models
> #38,-0.38309,-0.69929,0.60352,226.04,0.62032,0.28936,0.72902,38.256,-0.68443,0.65365,0.32294,241.06
> view matrix models
> #38,-0.34943,-0.72907,0.58852,222.05,0.61787,0.29288,0.72969,38.499,-0.70437,0.61861,0.34813,245.24
> view matrix models
> #38,-0.34943,-0.72907,0.58852,222.59,0.61787,0.29288,0.72969,38.714,-0.70437,0.61861,0.34813,242.8
> fitmap #38 inMap #46
Fit molecule 9hud (#38) to map cryosparc_P483_J72_006_volume_map.mrc (#46)
using 6282 atoms
average map value = 0.0399, steps = 112
shifted from previous position = 6.23
rotated from previous position = 3.87 degrees
atoms outside contour = 3940, contour level = 0.048075
Position of 9hud (#38) relative to cryosparc_P483_J72_006_volume_map.mrc (#46)
coordinates:
Matrix rotation and translation
-0.34701016 -0.76389374 0.54410505 226.91723804
0.57651318 0.28385608 0.76619729 40.13005322
-0.73974084 0.57956197 0.34189387 251.72894877
Axis -0.10005014 0.68823502 0.71855586
Axis point 172.83638513 16.61736328 0.00000000
Rotation angle (degrees) 111.13889774
Shift along axis 185.79711858
> select subtract #38
Nothing selected
> volume flip #46 axis z
Opened cryosparc_P483_J72_006_volume_map.mrc z flip as #47, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> select add #38
6282 atoms, 6138 bonds, 1077 residues, 1 model selected
> view matrix models
> #38,-0.43781,-0.43705,0.78569,225.72,0.89875,-0.18935,0.39548,11.956,-0.024068,0.87928,0.47569,125.36
> view matrix models
> #38,0.17782,0.26753,0.947,99.291,0.050808,-0.96355,0.26266,177.44,0.98275,0.001409,-0.18493,8.0567
> view matrix models
> #38,0.17782,0.26753,0.947,103.63,0.050808,-0.96355,0.26266,172.68,0.98275,0.001409,-0.18493,-1.716
> view matrix models
> #38,0.63642,0.20154,0.74455,36.153,-0.42467,-0.71425,0.55633,234.65,0.64391,-0.67025,-0.36898,79.951
> view matrix models
> #38,0.63642,0.20154,0.74455,34.766,-0.42467,-0.71425,0.55633,241.95,0.64391,-0.67025,-0.36898,57.4
> fitmap #38 inMap #47
Fit molecule 9hud (#38) to map cryosparc_P483_J72_006_volume_map.mrc z flip
(#47) using 6282 atoms
average map value = 0.06343, steps = 124
shifted from previous position = 5.23
rotated from previous position = 14 degrees
atoms outside contour = 2477, contour level = 0.048075
Position of 9hud (#38) relative to cryosparc_P483_J72_006_volume_map.mrc z
flip (#47) coordinates:
Matrix rotation and translation
0.48056680 0.06585233 0.87448215 60.37965921
-0.56537086 -0.73901641 0.36634758 262.76707770
0.67038150 -0.67046120 -0.31791576 52.06857630
Axis -0.84232947 0.16581649 -0.51282156
Axis point 0.00000000 144.40291810 -47.17976586
Rotation angle (degrees) 142.01600325
Shift along axis -33.99034036
> select subtract #38
Nothing selected
> hide #!47 models
> show #!47 models
> hide #!38 models
> show #!38 models
> hide #!38 models
> hide #!45 models
> show #!44 models
> show #!38 models
> select add #38
6282 atoms, 6138 bonds, 1077 residues, 1 model selected
> view matrix models
> #38,0.48057,0.065852,0.87448,65.866,-0.56537,-0.73902,0.36635,260.8,0.67038,-0.67046,-0.31792,67.074
> view matrix models
> #38,0.24561,0.13628,0.95974,99.26,-0.61016,-0.7476,0.2623,269.51,0.75324,-0.65002,-0.10047,50.465
> view matrix models
> #38,0.24561,0.13628,0.95974,97.908,-0.61016,-0.7476,0.2623,267.42,0.75324,-0.65002,-0.10047,51.929
> fitmap #38 inMap #44
Fit molecule 9hud (#38) to map cryosparc_P483_J81_008_volume_map.mrc z flip
(#44) using 6282 atoms
average map value = 0.03783, steps = 168
shifted from previous position = 5.42
rotated from previous position = 16.7 degrees
atoms outside contour = 3802, contour level = 0.040419
Position of 9hud (#38) relative to cryosparc_P483_J81_008_volume_map.mrc z
flip (#44) coordinates:
Matrix rotation and translation
0.06820670 -0.05795023 0.99598676 133.26750912
-0.73706857 -0.67572583 0.01115934 290.51260544
0.67236729 -0.73487167 -0.08880232 64.60372631
Axis -0.70414963 0.30545181 -0.64099336
Axis point 0.00000000 181.24183814 -90.37493056
Rotation angle (degrees) 148.01217964
Shift along axis -46.51322447
> select subtract #38
Nothing selected
> hide #!44 models
> show #!43 models
> transparency #38 50
> transparency #43 50
> select add #38
6282 atoms, 6138 bonds, 1077 residues, 1 model selected
> view matrix models
> #38,-0.34778,-0.62711,0.69698,224.64,0.7034,0.317,0.6362,16.77,-0.61991,0.71151,0.33086,208.25
> view matrix models
> #38,-0.34778,-0.62711,0.69698,225.83,0.7034,0.317,0.6362,17.542,-0.61991,0.71151,0.33086,207.48
> view matrix models
> #38,-0.28771,-0.41373,0.86374,206.06,0.80892,0.37784,0.45043,0.83954,-0.51271,0.82829,0.22596,187.36
> view matrix models
> #38,-0.28771,-0.41373,0.86374,206.43,0.80892,0.37784,0.45043,-2.4203,-0.51271,0.82829,0.22596,194.27
> view matrix models
> #38,-0.43329,-0.6387,0.63587,240.94,0.33837,0.53864,0.77161,61.821,-0.83533,0.54948,-0.01727,259.04
> view matrix models
> #38,-0.43329,-0.6387,0.63587,240.15,0.33837,0.53864,0.77161,62.236,-0.83533,0.54948,-0.01727,256.27
> view matrix models
> #38,-0.10971,-0.34204,0.93326,173.87,0.39597,0.84616,0.35667,46.512,-0.91169,0.40867,0.042608,273
> view matrix models
> #38,-0.10971,-0.34204,0.93326,174.05,0.39597,0.84616,0.35667,43.272,-0.91169,0.40867,0.042608,270.13
> hide #!43 models
> show #!44 models
> view matrix models
> #38,0.33372,0.10106,0.93724,86.86,-0.90444,-0.24596,0.34856,290.96,0.26575,-0.964,0.009315,136.98
> view matrix models
> #38,-0.0077799,0.047421,0.99884,142.16,-0.55565,-0.83068,0.035109,262.15,0.83138,-0.55473,0.032812,31.52
> view matrix models
> #38,-0.0077799,0.047421,0.99884,141.96,-0.55565,-0.83068,0.035109,262.22,0.83138,-0.55473,0.032812,29.958
> fitmap #38 inMap #44
Fit molecule 9hud (#38) to map cryosparc_P483_J81_008_volume_map.mrc z flip
(#44) using 6282 atoms
average map value = 0.03751, steps = 112
shifted from previous position = 5.86
rotated from previous position = 9.02 degrees
atoms outside contour = 3835, contour level = 0.040419
Position of 9hud (#38) relative to cryosparc_P483_J81_008_volume_map.mrc z
flip (#44) coordinates:
Matrix rotation and translation
0.05690807 -0.02329864 0.99810753 137.02419950
-0.65514588 -0.75524488 0.01972424 280.23565345
0.75335606 -0.65502851 -0.05824354 46.13973405
Axis -0.70561938 0.25594766 -0.66075116
Axis point 0.00000000 166.68305562 -94.19367789
Rotation angle (degrees) 151.43679087
Shift along axis -55.44815397
> select subtract #38
Nothing selected
> select add #38
6282 atoms, 6138 bonds, 1077 residues, 1 model selected
> view matrix models
> #38,-0.54924,-0.83446,0.044834,275.94,-0.071518,-0.0065171,-0.99742,171.91,0.8326,-0.55103,-0.0561,29.588
> view matrix models
> #38,-0.095818,-0.5899,-0.80177,205.42,-0.19261,0.80124,-0.56649,154.68,0.97659,0.10015,-0.1904,-16.494
> view matrix models
> #38,-0.39728,-0.77299,0.49462,243.92,-0.63802,-0.15476,-0.75431,264.16,0.65962,-0.61525,-0.4317,64.108
> view matrix models
> #38,0.28514,0.071787,0.95579,97.806,-0.70813,-0.65625,0.26054,281.81,0.64594,-0.75112,-0.13629,67.792
> view matrix models
> #38,0.28514,0.071787,0.95579,96.286,-0.70813,-0.65625,0.26054,282.4,0.64594,-0.75112,-0.13629,66.958
> fitmap #38 inMap #44
Fit molecule 9hud (#38) to map cryosparc_P483_J81_008_volume_map.mrc z flip
(#44) using 6282 atoms
average map value = 0.03783, steps = 168
shifted from previous position = 3.71
rotated from previous position = 14.8 degrees
atoms outside contour = 3801, contour level = 0.040419
Position of 9hud (#38) relative to cryosparc_P483_J81_008_volume_map.mrc z
flip (#44) coordinates:
Matrix rotation and translation
0.06820710 -0.05791598 0.99598872 133.26635838
-0.73705893 -0.67573598 0.01118160 290.51125280
0.67237782 -0.73486504 -0.08877748 64.60105058
Axis -0.70414832 0.30543677 -0.64100197
Axis point 0.00000000 181.23877487 -90.37820158
Rotation angle (degrees) 148.01136342
Shift along axis -46.51586553
> select subtract #38
Nothing selected
> show #35 models
> select add #35
5953 atoms, 5684 bonds, 699 residues, 1 model selected
> view matrix models
> #35,-0.44103,0.30301,0.84479,116.92,-0.07491,-0.95043,0.30179,113.9,0.89436,0.069815,0.44187,126.48
> view matrix models
> #35,0.84908,-0.51887,-0.099238,120.01,0.43126,0.7893,-0.43705,123.08,0.3051,0.3283,0.89394,124.61
> mmaker #35 to #38
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 9hud, chain A (#38) with 8pi2, chain A (#35), sequence alignment
score = 1753.4
RMSD between 220 pruned atom pairs is 0.913 angstroms; (across all 331 pairs:
6.169)
> hide #!38 models
> fitmap #35 inMap #44
Fit molecule 8pi2 (#35) to map cryosparc_P483_J81_008_volume_map.mrc z flip
(#44) using 5953 atoms
average map value = 0.03426, steps = 124
shifted from previous position = 5.39
rotated from previous position = 16.8 degrees
atoms outside contour = 3776, contour level = 0.040419
Position of 8pi2 (#35) relative to cryosparc_P483_J81_008_volume_map.mrc z
flip (#44) coordinates:
Matrix rotation and translation
-0.91986475 0.28876257 0.26545250 167.24012801
0.39170890 0.64122785 0.65984164 130.22015692
0.02032204 0.71094517 -0.70295376 131.41006954
Axis 0.18875717 0.90541952 0.38024495
Axis point 72.13306632 0.00000000 33.49476567
Rotation angle (degrees) 172.22007439
Shift along axis 199.43966055
> mmaker #35 to #38
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 9hud, chain A (#38) with 8pi2, chain A (#35), sequence alignment
score = 1753.4
RMSD between 220 pruned atom pairs is 0.913 angstroms; (across all 331 pairs:
6.169)
> select subtract #35
Nothing selected
> hide #!44 models
> show #!44 models
> hide #35 models
> show #!38 models
> show #!37 models
> mmaker #37 to #38
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 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
score = 1674.4
RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
0.519)
> hide #!38 models
> show #!38 models
> hide #!37 models
> hide #!38 models
> hide #!44 models
> show #!47 models
> show #!38 models
> select add #38
6282 atoms, 6138 bonds, 1077 residues, 1 model selected
> view matrix models
> #38,0.12454,-0.84591,0.51858,160.56,-0.95063,-0.25145,-0.18186,310.42,0.28423,-0.47033,-0.83547,125.18
> view matrix models
> #38,0.67023,0.035917,0.74129,37.629,-0.48282,-0.73746,0.47227,246.9,0.56363,-0.67443,-0.47692,84.334
> view matrix models
> #38,0.67023,0.035917,0.74129,35.095,-0.48282,-0.73746,0.47227,252.87,0.56363,-0.67443,-0.47692,70.069
> view matrix models
> #38,0.72811,0.043332,0.68409,26.371,-0.55319,-0.55218,0.62376,255,0.40477,-0.8326,-0.37807,100.03
> view matrix models
> #38,0.72811,0.043332,0.68409,24.921,-0.55319,-0.55218,0.62376,251.59,0.40477,-0.8326,-0.37807,100.94
> fitmap #38 inMap #47
Fit molecule 9hud (#38) to map cryosparc_P483_J72_006_volume_map.mrc z flip
(#47) using 6282 atoms
average map value = 0.06343, steps = 212
shifted from previous position = 1.3
rotated from previous position = 22.3 degrees
atoms outside contour = 2481, contour level = 0.048075
Position of 9hud (#38) relative to cryosparc_P483_J72_006_volume_map.mrc z
flip (#47) coordinates:
Matrix rotation and translation
0.48048529 0.06576118 0.87453379 60.39061577
-0.56539285 -0.73906673 0.36621209 262.77340318
0.67042137 -0.67041468 -0.31792978 52.06026777
Axis -0.84230945 0.16585123 -0.51284322
Axis point 0.00000000 144.40605826 -47.18056764
Rotation angle (degrees) 142.02279334
Shift along axis -33.98504950
> select subtract #38
Nothing selected
> volume #47 level 0.05522
> volume #47 level 0.04807
> show #!37 models
> mmaker #37 to #38
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 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
score = 1674.4
RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
0.519)
> volume #47 level 0.0495
> volume #47 level 0.01949
> volume #47 level 0.02878
> volume gaussian #47 sDev 2
Opened cryosparc_P483_J72_006_volume_map.mrc z flip gaussian as #48, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> volume #48 level 0.002656
> volume #48 level 0.001381
> surface dust #48 size 7.23
> show #!44 models
> hide #!38 models
> hide #!37 models
> volume gaussian #44 sDev 2
Opened cryosparc_P483_J81_008_volume_map.mrc z flip gaussian as #49, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> surface dust #49 size 7.23
> volume #49 level 0.01018
Cell requested for row 3 is out of bounds for table with 3 rows! Resizing
table model.
> save "/Users/amy/Desktop/SPA AAT_HNE/9C5_Fab_AAT_HNE/For mask
> generation/hne_J81localrefine.mrc" models #49
> volume #49 level 0.01049
> open /Users/amy/Downloads/cryosparc_P483_J82_005_volume_map.mrc
Opened cryosparc_P483_J82_005_volume_map.mrc as #50, grid size 400,400,400,
pixel 0.723, shown at level 0.00546, step 2, values float32
> volume #50 level 0.0526
> open /Users/amy/Downloads/cryosparc_P483_J90_004_volume_map.mrc
Opened cryosparc_P483_J90_004_volume_map.mrc as #51, grid size 400,400,400,
pixel 0.723, shown at level 0.00654, step 2, values float32
> surface dust #51 size 7.23
> volume #51 level 0.03836
> open /Users/amy/Downloads/cryosparc_P483_J89_003_volume_map.mrc
Opened cryosparc_P483_J89_003_volume_map.mrc as #52, grid size 400,400,400,
pixel 0.723, shown at level 0.00398, step 2, values float32
> volume #52 level 0.01728
> volume #52 level 0.004928
> hide #!52 models
> show #!44 models
> open /Users/amy/Downloads/cryosparc_P483_J93_005_volume_map.mrc
Opened cryosparc_P483_J93_005_volume_map.mrc as #53, grid size 400,400,400,
pixel 0.723, shown at level 0.00624, step 2, values float32
> volume #53 level 0.03597
> open /Users/amy/Downloads/cryosparc_P483_J96_002_volume_map.mrc
Opened cryosparc_P483_J96_002_volume_map.mrc as #54, grid size 400,400,400,
pixel 0.723, shown at level 0.00203, step 2, values float32
> volume #54 level 0.01882
> volume #54 level 0.01406
> open /Users/amy/Downloads/cryosparc_P483_J99_003_volume_map.mrc
Opened cryosparc_P483_J99_003_volume_map.mrc as #55, grid size 400,400,400,
pixel 0.723, shown at level 0.00233, step 2, values float32
> surface dust #55 size 7.23
> volume #55 level 0.011
> ui mousemode right "tape measure"
> marker segment #56 position 137.9,161.4,84.92 toPosition 127.8,150.1,133.2
> color yellow radius 0.1807 label 50.59 labelHeight 5.059 labelColor yellow
> marker segment #56 position 137.6,155.7,84.27 toPosition 148.8,133.1,193.5
> color yellow radius 0.1807 label 112.1 labelHeight 11.21 labelColor yellow
> marker segment #56 position 139,177,192 toPosition 130,91.37,164 color
> yellow radius 0.1807 label 90.59 labelHeight 9.059 labelColor yellow
> close #56
> transparency #55 50
> show #!38 models
> select add #38
6282 atoms, 6138 bonds, 1077 residues, 1 model selected
> select subtract #38
Nothing selected
> volume flip #55 axis z
Opened cryosparc_P483_J99_003_volume_map.mrc z flip as #56, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> transparency #56 50
> select add #38
6282 atoms, 6138 bonds, 1077 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #38,0.48049,0.065761,0.87453,61.743,-0.56539,-0.73907,0.36621,262.06,0.67042,-0.67041,-0.31793,59.233
> view matrix models
> #38,0.61181,-0.23623,0.75491,54.055,-0.64298,-0.70439,0.30068,273.82,0.46072,-0.66935,-0.58285,95.671
> view matrix models
> #38,0.50154,0.032674,0.86452,59.807,-0.035285,-0.99768,0.058177,191.99,0.86441,-0.059683,-0.49923,7.3804
> view matrix models
> #38,0.50154,0.032674,0.86452,52.131,-0.035285,-0.99768,0.058177,176.02,0.86441,-0.059683,-0.49923,12.857
> view matrix models
> #38,0.35345,0.1643,0.92091,69.799,-0.028974,-0.98206,0.18633,172.82,0.93501,-0.09254,-0.34235,0.99177
> view matrix models
> #38,0.66671,0.39133,0.63431,15.122,-0.22913,-0.70224,0.67407,187.64,0.70922,-0.59475,-0.37853,56.427
> view matrix models
> #38,0.66671,0.39133,0.63431,20.436,-0.22913,-0.70224,0.67407,208.21,0.70922,-0.59475,-0.37853,56.608
> view matrix models
> #38,0.81008,0.3223,0.48979,2.2149,-0.16331,-0.67827,0.71643,196.35,0.56311,-0.66036,-0.49682,83.714
> fitmap #38 inMap #56
Fit molecule 9hud (#38) to map cryosparc_P483_J99_003_volume_map.mrc z flip
(#56) using 6282 atoms
average map value = 0.03831, steps = 132
shifted from previous position = 1.92
rotated from previous position = 15.8 degrees
atoms outside contour = 568, contour level = 0.011004
Position of 9hud (#38) relative to cryosparc_P483_J99_003_volume_map.mrc z
flip (#56) coordinates:
Matrix rotation and translation
0.71987433 0.56582857 0.40201864 5.33395219
-0.00113467 -0.57823035 0.81587277 166.00801694
0.69410350 -0.58778202 -0.41561115 58.96322716
Axis -0.91042678 -0.18944963 -0.36773893
Axis point 0.00000000 92.18313505 -11.68775993
Rotation angle (degrees) 129.56725904
Shift along axis -57.98940372
> select subtract #38
Nothing selected
> show #!37 models
> mmaker #38 to #37
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 1ezx, chain A (#37) with 9hud, chain A (#38), sequence alignment
score = 1674.4
RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
0.519)
> select add #38
6282 atoms, 6138 bonds, 1077 residues, 1 model selected
> view matrix models
> #38,0.48049,0.065761,0.87453,62.141,-0.56539,-0.73907,0.36621,264.84,0.67042,-0.67041,-0.31793,61.109
> view matrix models
> #38,0.48049,0.065761,0.87453,61.431,-0.56539,-0.73907,0.36621,264.59,0.67042,-0.67041,-0.31793,64.599
> fitmap #38 inMap #56
Fit molecule 9hud (#38) to map cryosparc_P483_J99_003_volume_map.mrc z flip
(#56) using 6282 atoms
average map value = 0.03831, steps = 216
shifted from previous position = 1.65
rotated from previous position = 43.4 degrees
atoms outside contour = 569, contour level = 0.011004
Position of 9hud (#38) relative to cryosparc_P483_J99_003_volume_map.mrc z
flip (#56) coordinates:
Matrix rotation and translation
0.71990687 0.56573446 0.40209280 5.32940054
-0.00119592 -0.57831351 0.81581374 166.01905071
0.69406964 -0.58779078 -0.41565530 58.96739860
Axis -0.91044042 -0.18938918 -0.36773629
Axis point 0.00000000 92.19051844 -11.68521420
Rotation angle (degrees) 129.57078110
Shift along axis -57.97876700
> select subtract #38
Nothing selected
> show #!39 models
> hide #!39 models
> show #!37 models
> mmaker #37 to #38
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 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
score = 1674.4
RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
0.519)
> volume #56 level 0.007481
> show #!42 models
> hide #!42 models
> combine #37 close false
> hide #!57.1 models
> hide #!37 models
> show #!37 models
> hide #!38 models
> hide #!37 models
> select #57/A
2686 atoms, 2674 bonds, 398 residues, 1 model selected
> delete #57/A
> select #57/B
289 atoms, 294 bonds, 39 residues, 1 model selected
> delete #57/B
> show #!37 models
> show #!38 models
> fitmap #57 inMap #56
Fit molecule copy of 1ezx (#57) to map cryosparc_P483_J99_003_volume_map.mrc z
flip (#56) using 1009 atoms
average map value = 0.01739, steps = 256
shifted from previous position = 13.8
rotated from previous position = 53.3 degrees
atoms outside contour = 290, contour level = 0.0074814
Position of copy of 1ezx (#57) relative to
cryosparc_P483_J99_003_volume_map.mrc z flip (#56) coordinates:
Matrix rotation and translation
0.75779051 -0.13010105 0.63939601 57.96350024
0.04649693 0.98819623 0.14596657 79.83854912
-0.65083914 -0.08088213 0.75489502 138.89870189
Axis -0.17161128 0.97606430 0.13359657
Axis point 208.75729766 0.00000000 -34.80031847
Rotation angle (degrees) 41.37141702
Shift along axis 86.53675668
> hide #!38 models
> hide #!37 models
> show #!37 models
> hide #!37 models
> show #!38 models
> show #!47 models
> hide #!56 models
> hide #!57 models
> hide #!47 models
> open /Users/amy/Downloads/cryosparc_P483_J103_003_volume_map.mrc
Opened cryosparc_P483_J103_003_volume_map.mrc as #58, grid size 400,400,400,
pixel 0.723, shown at level 0.00468, step 2, values float32
> surface dust #58 size 7.23
> volume #58 level 0.01873
> transparency #58 50
> select add #38
6282 atoms, 6138 bonds, 1077 residues, 1 model selected
> view matrix models
> #38,0.79207,-0.60151,-0.10399,45.033,0.096519,-0.044809,0.99432,127.86,-0.60276,-0.79761,0.022565,266.66
> view matrix models
> #38,-0.14652,-0.85779,0.49268,195.86,0.54759,0.34445,0.76256,44.475,-0.82382,0.38152,0.41925,251.42
> view matrix models
> #38,-0.14652,-0.85779,0.49268,198.48,0.54759,0.34445,0.76256,48.533,-0.82382,0.38152,0.41925,263.76
> view matrix models
> #38,-0.14652,-0.85779,0.49268,194.13,0.54759,0.34445,0.76256,44.618,-0.82382,0.38152,0.41925,261.43
> view matrix models
> #38,-0.10749,-0.76087,0.63994,182.4,0.68336,0.41097,0.60342,22.58,-0.72212,0.50217,0.47577,240.01
> volume flip #58 axis z
Opened cryosparc_P483_J103_003_volume_map.mrc z flip as #59, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> view matrix models
> #38,0.47388,0.52578,0.70639,40.242,-0.49413,-0.50521,0.70753,242.68,0.72888,-0.68433,0.020401,61.728
> view matrix models
> #38,0.47388,0.52578,0.70639,38.39,-0.49413,-0.50521,0.70753,241.35,0.72888,-0.68433,0.020401,61.925
> view matrix models
> #38,0.62595,0.63777,0.44881,13.26,-0.13423,-0.47881,0.8676,181.41,0.76822,-0.60332,-0.2141,55.525
> view matrix models
> #38,0.62595,0.63777,0.44881,16.43,-0.13423,-0.47881,0.8676,181.76,0.76822,-0.60332,-0.2141,47.364
> view matrix models
> #38,0.62595,0.63777,0.44881,20.934,-0.13423,-0.47881,0.8676,183.19,0.76822,-0.60332,-0.2141,39.547
> fitmap #38 inMap #59
Fit molecule 9hud (#38) to map cryosparc_P483_J103_003_volume_map.mrc z flip
(#59) using 6282 atoms
average map value = 0.04126, steps = 168
shifted from previous position = 5.69
rotated from previous position = 19.5 degrees
atoms outside contour = 1297, contour level = 0.018732
Position of 9hud (#38) relative to cryosparc_P483_J103_003_volume_map.mrc z
flip (#59) coordinates:
Matrix rotation and translation
0.70777878 0.35342642 0.61166899 13.30926304
-0.29975381 -0.63379066 0.71306173 215.20863100
0.63968496 -0.68804008 -0.34264266 66.23170214
Axis -0.90619968 -0.01812007 -0.42246160
Axis point 0.00000000 119.91219967 -25.94584346
Rotation angle (degrees) 129.37010768
Shift along axis -43.94079555
> mmaker #37 to #38
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 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
score = 1674.4
RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
0.519)
> select subtract #38
Nothing selected
> show #!37 models
> show #!57 models
> mmaker #57 to #37
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 1ezx, chain C (#37) with copy of 1ezx, chain C (#57), sequence
alignment score = 1096
RMSD between 140 pruned atom pairs is 0.000 angstroms; (across all 140 pairs:
0.000)
> hide #!37 models
> select #57/A
Nothing selected
> select #57/C
1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 2 models selected
> select #57/C: 202
6 atoms, 5 bonds, 1 residue, 1 model selected
> show #!37 models
> ui tool show "Show Sequence Viewer"
> select #57/C: 197
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #57/C: 195
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #57
1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 3 models selected
> select subtract #57
Nothing selected
> hide #!37 models
> select add #57
1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 3 models selected
> fitmap #57 inMap #59
Fit molecule copy of 1ezx (#57) to map cryosparc_P483_J103_003_volume_map.mrc
z flip (#59) using 1009 atoms
average map value = 0.03856, steps = 332
shifted from previous position = 30.6
rotated from previous position = 62.2 degrees
atoms outside contour = 286, contour level = 0.018732
Position of copy of 1ezx (#57) relative to
cryosparc_P483_J103_003_volume_map.mrc z flip (#59) coordinates:
Matrix rotation and translation
0.57046373 0.04988227 0.81980662 55.55575937
-0.78184304 0.33872670 0.52343642 167.07972587
-0.25158019 -0.93956159 0.23223140 158.05911115
Axis -0.73333465 0.53703769 -0.41690623
Axis point 0.00000000 214.40037540 -65.68721584
Rotation angle (degrees) 85.94517935
Shift along axis -16.90868204
> view matrix models
> #57,0.57046,0.049882,0.81981,53.391,-0.78184,0.33873,0.52344,146.96,-0.25158,-0.93956,0.23223,152.39
> view matrix models
> #57,0.57046,0.049882,0.81981,51.548,-0.78184,0.33873,0.52344,139.36,-0.25158,-0.93956,0.23223,150.37
> view matrix models
> #57,0.60961,0.26554,0.74691,47.106,-0.77216,0.41204,0.48373,138.91,-0.17931,-0.87162,0.45622,131.48
> view matrix models
> #57,0.60961,0.26554,0.74691,46.208,-0.77216,0.41204,0.48373,140.83,-0.17931,-0.87162,0.45622,128.81
> view matrix models
> #57,0.49766,0.67771,0.54133,56.234,-0.85191,0.49924,0.15817,161.92,-0.16306,-0.53988,0.8258,100.9
> view matrix models
> #57,0.49766,0.67771,0.54133,55.941,-0.85191,0.49924,0.15817,159.37,-0.16306,-0.53988,0.8258,99.317
> view matrix models
> #57,0.83968,0.36634,0.40093,42.637,-0.49094,0.82767,0.27193,116.69,-0.23222,-0.42516,0.87482,99.752
> hide #!57 models
> select subtract #57
Nothing selected
> hide #!59 models
> show #!47 models
> fitmap #38 inMap #47
Fit molecule 9hud (#38) to map cryosparc_P483_J72_006_volume_map.mrc z flip
(#47) using 6282 atoms
average map value = 0.06343, steps = 180
shifted from previous position = 8.63
rotated from previous position = 26.1 degrees
atoms outside contour = 1606, contour level = 0.028781
Position of 9hud (#38) relative to cryosparc_P483_J72_006_volume_map.mrc z
flip (#47) coordinates:
Matrix rotation and translation
0.48062832 0.06570846 0.87445915 60.38102135
-0.56537857 -0.73904318 0.36628165 262.76806751
0.67033088 -0.67044580 -0.31805493 52.08064169
Axis -0.84235493 0.16585696 -0.51276666
Axis point 0.00000000 144.40697546 -47.16273001
Rotation angle (degrees) 142.02086420
Shift along axis -33.98555515
> show #35 models
> mmaker #35 to #38
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 9hud, chain A (#38) with 8pi2, chain A (#35), sequence alignment
score = 1753.4
RMSD between 220 pruned atom pairs is 0.913 angstroms; (across all 331 pairs:
6.169)
> hide #!38 models
> show #!38 models
> hide #35 models
> show #35 models
> hide #35 models
> show #35 models
> hide #35 models
> hide #!38 models
> hide #!47 models
> show #!59 models
> open cryosparc_P483_J70_00018_volume_series vseries true
'cryosparc_P483_J70_00018_volume_series' has no suffix
> open
> /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_00_00018_volume.mrc
> /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_01_00018_volume.mrc
> /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_02_00018_volume.mrc
> /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_03_00018_volume.mrc
> /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_04_00018_volume.mrc
> /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_05_00018_volume.mrc
> /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_06_00018_volume.mrc
> /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_07_00018_volume.mrc
> /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_08_00018_volume.mrc
> /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_09_00018_volume.mrc
Opened J70_class_00_00018_volume.mrc as #60.1, grid size 64,64,64, pixel 4.52,
shown at level 0.113, step 1, values float32
Opened J70_class_01_00018_volume.mrc as #60.2, grid size 64,64,64, pixel 4.52,
shown at level 0.104, step 1, values float32
Opened J70_class_02_00018_volume.mrc as #60.3, grid size 64,64,64, pixel 4.52,
shown at level 0.109, step 1, values float32
Opened J70_class_03_00018_volume.mrc as #60.4, grid size 64,64,64, pixel 4.52,
shown at level 0.116, step 1, values float32
Opened J70_class_04_00018_volume.mrc as #60.5, grid size 64,64,64, pixel 4.52,
shown at level 0.106, step 1, values float32
Opened J70_class_05_00018_volume.mrc as #60.6, grid size 64,64,64, pixel 4.52,
shown at level 0.106, step 1, values float32
Opened J70_class_06_00018_volume.mrc as #60.7, grid size 64,64,64, pixel 4.52,
shown at level 0.116, step 1, values float32
Opened J70_class_07_00018_volume.mrc as #60.8, grid size 64,64,64, pixel 4.52,
shown at level 0.109, step 1, values float32
Opened J70_class_08_00018_volume.mrc as #60.9, grid size 64,64,64, pixel 4.52,
shown at level 0.106, step 1, values float32
Opened J70_class_09_00018_volume.mrc as #60.10, grid size 64,64,64, pixel
4.52, shown at level 0.113, step 1, values float32
> hide #!59 models
> surface dust #60.1 size 45.2
> surface dust #60.2 size 45.2
> surface dust #60.3 size 45.2
> surface dust #60.4 size 45.2
> surface dust #60.5 size 45.2
> surface dust #60.6 size 45.2
> surface dust #60.7 size 45.2
> surface dust #60.8 size 45.2
> surface dust #60.9 size 45.2
> surface dust #60.10 size 45.2
> hide #!60.1 models
> hide #!60.2 models
> hide #!60.3 models
> hide #!60.4 models
> hide #!60.5 models
> hide #!60.6 models
> hide #!60.7 models
> hide #!60.8 models
> hide #!60.9 models
> hide #!60.10 models
> show #!60.1 models
> show #!60.2 models
> hide #!60.1 models
> hide #!60.2 models
> show #!60.3 models
> show #!60.2 models
> hide #!60.2 models
> show #!60.4 models
> hide #!60.3 models
> show #!60.5 models
> hide #!60.4 models
> show #!60.6 models
> hide #!60.5 models
> show #!60.7 models
> hide #!60.6 models
> show #!60.8 models
> hide #!60.7 models
> show #!60.9 models
> hide #!60.8 models
> show #!60.10 models
> hide #!60.9 models
> hide #!60 target m
[Repeated 1 time(s)]
> close #60
> open
> /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_00_00020_volume.mrc
> /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_01_00020_volume.mrc
> /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_02_00020_volume.mrc
> /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_03_00020_volume.mrc
> /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_04_00020_volume.mrc
> /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_05_00020_volume.mrc
> /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_06_00020_volume.mrc
> /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_07_00020_volume.mrc
> /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_08_00020_volume.mrc
> /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_09_00020_volume.mrc
Opened J124_class_00_00020_volume.mrc as #60.1, grid size 64,64,64, pixel
4.52, shown at level 0.058, step 1, values float32
Opened J124_class_01_00020_volume.mrc as #60.2, grid size 64,64,64, pixel
4.52, shown at level 0.0583, step 1, values float32
Opened J124_class_02_00020_volume.mrc as #60.3, grid size 64,64,64, pixel
4.52, shown at level 0.0581, step 1, values float32
Opened J124_class_03_00020_volume.mrc as #60.4, grid size 64,64,64, pixel
4.52, shown at level 0.0576, step 1, values float32
Opened J124_class_04_00020_volume.mrc as #60.5, grid size 64,64,64, pixel
4.52, shown at level 0.0607, step 1, values float32
Opened J124_class_05_00020_volume.mrc as #60.6, grid size 64,64,64, pixel
4.52, shown at level 0.0608, step 1, values float32
Opened J124_class_06_00020_volume.mrc as #60.7, grid size 64,64,64, pixel
4.52, shown at level 0.0585, step 1, values float32
Opened J124_class_07_00020_volume.mrc as #60.8, grid size 64,64,64, pixel
4.52, shown at level 0.0573, step 1, values float32
Opened J124_class_08_00020_volume.mrc as #60.9, grid size 64,64,64, pixel
4.52, shown at level 0.0591, step 1, values float32
Opened J124_class_09_00020_volume.mrc as #60.10, grid size 64,64,64, pixel
4.52, shown at level 0.0602, step 1, values float32
> surface dust #60.1 size 45.2
> surface dust #60.2 size 45.2
> surface dust #60.3 size 45.2
> surface dust #60.4 size 45.2
> surface dust #60.5 size 45.2
> surface dust #60.6 size 45.2
> surface dust #60.7 size 45.2
> surface dust #60.8 size 45.2
> surface dust #60.9 size 45.2
> surface dust #60.10 size 45.2
> hide #!60 models
> show #!60 models
> hide #!60.1 models
> hide #!60.2 models
> hide #!60.3 models
> hide #!60.4 models
> hide #!60.5 models
> hide #!60.6 models
> hide #!60.7 models
> hide #!60.8 models
> hide #!60.9 models
> hide #!60.10 models
> show #!60.1 models
> show #!60.2 models
> hide #!60.1 models
> show #!60.3 models
> hide #!60.2 models
> show #!60.4 models
> hide #!60.3 models
> show #!60.5 models
> hide #!60.4 models
> show #!60.6 models
> hide #!60.5 models
> show #!60.7 models
> hide #!60.6 models
> show #!60.8 models
> hide #!60.7 models
> show #!60.9 models
> hide #!60.8 models
> show #!60.10 models
> hide #!60.9 models
> hide #!60.10 models
> open /Users/amy/Downloads/cryosparc_P483_J131_007_volume_map.mrc
Opened cryosparc_P483_J131_007_volume_map.mrc as #61, grid size 400,400,400,
pixel 0.723, shown at level 0.00743, step 2, values float32
> volume #61 level 0.0358
> transparency #61 50
Cell requested for row 59 is out of bounds for table with 71 rows! Resizing
table model.
> close #60
> show #!57 models
> hide #!57 models
> show #!38 models
> select add #38
6282 atoms, 6138 bonds, 1077 residues, 1 model selected
> view matrix models
> #38,0.28938,-0.95095,0.1093,139.21,-0.034645,0.10371,0.994,138.64,-0.95659,-0.29143,-0.0029341,290.92
> view matrix models
> #38,-0.45918,-0.73297,0.50191,244.33,0.66345,0.092766,0.74245,31.785,-0.59075,0.67391,0.44369,190.43
> view matrix models
> #38,-0.45918,-0.73297,0.50191,252.99,0.66345,0.092766,0.74245,27.709,-0.59075,0.67391,0.44369,215.88
> view matrix models
> #38,-0.45918,-0.73297,0.50191,245.4,0.66345,0.092766,0.74245,38.203,-0.59075,0.67391,0.44369,230.11
> view matrix models
> #38,0.7804,-0.38868,0.4898,36.281,-0.57699,-0.14577,0.80364,242.79,-0.24096,-0.90977,-0.33802,245.32
> view matrix models
> #38,0.24076,-0.088229,0.96657,104.14,-0.7449,-0.65522,0.12574,297.37,0.62222,-0.75027,-0.22348,101.24
> view matrix models
> #38,0.24076,-0.088229,0.96657,102.45,-0.7449,-0.65522,0.12574,304,0.62222,-0.75027,-0.22348,88.677
> volume flip #61 axis z
Opened cryosparc_P483_J131_007_volume_map.mrc z flip as #60, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> view matrix models
> #38,0.24076,-0.088229,0.96657,101.92,-0.7449,-0.65522,0.12574,291.88,0.62222,-0.75027,-0.22348,62.156
> view matrix models
> #38,0.44059,0.20906,0.87303,60.073,-0.32965,-0.86689,0.37395,231.22,0.83499,-0.45255,-0.31303,18.198
> view matrix models
> #38,0.44059,0.20906,0.87303,63.215,-0.32965,-0.86689,0.37395,234.58,0.83499,-0.45255,-0.31303,17.855
> fitmap #38 inMap #61
Fit molecule 9hud (#38) to map cryosparc_P483_J131_007_volume_map.mrc (#61)
using 6282 atoms
average map value = 0.03062, steps = 228
shifted from previous position = 12.1
rotated from previous position = 10.2 degrees
atoms outside contour = 4063, contour level = 0.0358
Position of 9hud (#38) relative to cryosparc_P483_J131_007_volume_map.mrc
(#61) coordinates:
Matrix rotation and translation
0.47633594 0.18597339 0.85937068 60.19776260
-0.46622754 -0.77523836 0.42618936 248.08769926
0.74547700 -0.60367159 -0.28256798 49.22817896
Axis -0.84117201 0.09302633 -0.53270606
Axis point 0.00000000 131.55393794 -45.87457813
Rotation angle (degrees) 142.25427000
Shift along axis -53.78213480
> fitmap #38 inMap #60
Fit molecule 9hud (#38) to map cryosparc_P483_J131_007_volume_map.mrc z flip
(#60) using 6282 atoms
average map value = 0.07254, steps = 164
shifted from previous position = 12.4
rotated from previous position = 8.44 degrees
atoms outside contour = 1769, contour level = 0.0358
Position of 9hud (#38) relative to cryosparc_P483_J131_007_volume_map.mrc z
flip (#60) coordinates:
Matrix rotation and translation
0.48808324 0.07900810 0.86921371 58.92380628
-0.57432345 -0.72083004 0.38801627 263.44883633
0.65721178 -0.68859406 -0.30644886 54.98864316
Axis -0.84303960 0.16600809 -0.51159120
Axis point 0.00000000 145.56353638 -47.97475612
Rotation angle (degrees) 140.31778784
Shift along axis -34.07217072
> show #!37 models
> mmaker #37 to #38
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 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
score = 1674.4
RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
0.519)
> open /Users/amy/Downloads/cryosparc_P483_J128_006_volume_map.mrc
Opened cryosparc_P483_J128_006_volume_map.mrc as #62, grid size 400,400,400,
pixel 0.723, shown at level 0.00501, step 2, values float32
> select subtract #38
Nothing selected
> hide #!38 models
> hide #!37 models
> hide #!60 models
> hide #!62 models
> open /Users/amy/Downloads/cryosparc_P483_J137_003_volume_map.mrc
Opened cryosparc_P483_J137_003_volume_map.mrc as #63, grid size 400,400,400,
pixel 0.723, shown at level 0.00802, step 2, values float32
> volume #63 level 0.03618
> volume flip #63 axis z
Opened cryosparc_P483_J137_003_volume_map.mrc z flip as #64, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> transparency #63 50
> transparency #64 50
> show #!38 models
> select add #38
6282 atoms, 6138 bonds, 1077 residues, 1 model selected
> show #!63 models
> hide #!64 models
> view matrix models
> #38,0.48808,0.079008,0.86921,57.589,-0.57432,-0.72083,0.38802,273.61,0.65721,-0.68859,-0.30645,79.373
> view matrix models
> #38,0.2297,0.46473,0.85514,83.832,-0.58104,-0.6394,0.50355,270.11,0.78079,-0.61253,0.12316,51.538
> view matrix models
> #38,0.2297,0.46473,0.85514,85.324,-0.58104,-0.6394,0.50355,273.24,0.78079,-0.61253,0.12316,53.863
> view matrix models
> #38,0.39662,0.46965,0.78875,59.564,-0.57284,-0.54478,0.61243,266.95,0.71732,-0.69472,0.052964,67.932
> show #!64 models
> hide #!63 models
> view matrix models
> #38,-0.91348,-0.3347,0.23136,304.61,0.38224,-0.51103,0.7699,112.62,-0.13945,0.79172,0.59475,139.64
> view matrix models
> #38,-0.59049,-0.80568,-0.046958,275.08,-0.087884,0.0063535,0.99611,164.3,-0.80225,0.59232,-0.074558,260.49
> view matrix models
> #38,-0.59049,-0.80568,-0.046958,273.4,-0.087884,0.0063535,0.99611,163.84,-0.80225,0.59232,-0.074558,241.17
> view matrix models
> #38,-0.55648,-0.77337,0.3037,262.39,0.12542,0.28314,0.95084,120.04,-0.82134,0.56721,-0.060566,244.98
> fitmap #38 inMap #64
Fit molecule 9hud (#38) to map cryosparc_P483_J137_003_volume_map.mrc z flip
(#64) using 6282 atoms
average map value = 0.03426, steps = 96
shifted from previous position = 4.73
rotated from previous position = 4.41 degrees
atoms outside contour = 3712, contour level = 0.036179
Position of 9hud (#38) relative to cryosparc_P483_J137_003_volume_map.mrc z
flip (#64) coordinates:
Matrix rotation and translation
-0.57799196 -0.77115445 0.26691966 270.23868060
0.05229306 0.29141704 0.95516572 129.97421192
-0.81436523 0.56603615 -0.12811068 246.02921542
Axis -0.27524806 0.76483926 0.58245980
Axis point 198.55971177 0.00000000 -12.15810570
Rotation angle (degrees) 135.01912752
Shift along axis 168.32883368
> hide #!64 models
> show #!63 models
> view matrix models
> #38,0.28227,0.88622,0.36734,69.32,0.13351,-0.41547,0.89976,144.95,0.95,-0.20493,-0.23559,-2.1095
> view matrix models
> #38,0.28227,0.88622,0.36734,65.915,0.13351,-0.41547,0.89976,149,0.95,-0.20493,-0.23559,14.639
> view matrix models
> #38,-0.00068529,0.90537,0.42463,109.22,-0.0059164,-0.42462,0.90535,171.33,0.99998,-0.0018918,0.0056475,-4.0739
> fitmap #38 inMap #63
Fit molecule 9hud (#38) to map cryosparc_P483_J137_003_volume_map.mrc (#63)
using 6282 atoms
average map value = 0.03246, steps = 440
shifted from previous position = 6.15
rotated from previous position = 34.9 degrees
atoms outside contour = 3887, contour level = 0.036179
Position of 9hud (#38) relative to cryosparc_P483_J137_003_volume_map.mrc
(#63) coordinates:
Matrix rotation and translation
0.42909681 0.75362179 0.49792584 49.09248009
-0.38069938 -0.34900840 0.85630668 221.91213193
0.81911167 -0.55699852 0.13714496 46.28691655
Axis -0.76791055 -0.17451431 -0.61632632
Axis point -0.00000000 97.45467483 -84.23279059
Rotation angle (degrees) 113.04060047
Shift along axis -104.95332191
> hide #!63 models
> show #!64 models
> view matrix models
> #38,0.6404,-0.29362,0.70969,53.209,-0.098072,0.88521,0.45474,134.87,-0.76175,-0.36082,0.5381,283.79
> view matrix models
> #38,-0.26615,-0.29672,0.91713,194.12,0.6919,0.60364,0.39609,21.458,-0.67114,0.73998,0.044637,233.39
> view matrix models
> #38,0.42821,0.78395,0.44952,48.675,0.43344,0.2583,-0.86337,91.334,-0.79295,0.56454,-0.22919,262.81
> view matrix models
> #38,0.40387,0.68567,-0.6056,69.485,-0.40554,-0.4592,-0.79036,250.65,-0.82002,0.5648,0.092606,263.06
> view matrix models
> #38,-0.85722,-0.30291,-0.41645,304.52,-0.2744,-0.41565,0.86714,207.52,-0.43576,0.8576,0.27319,188.79
> view matrix models
> #38,-0.57679,-0.55417,0.60017,257.1,0.51884,0.31896,0.79314,54.792,-0.63097,0.76887,0.10355,225.19
> view matrix models
> #38,-0.57679,-0.55417,0.60017,254.28,0.51884,0.31896,0.79314,61.36,-0.63097,0.76887,0.10355,204.28
> view matrix models
> #38,-0.60566,-0.70889,0.36146,267.77,0.21101,0.29491,0.93193,109.24,-0.76724,0.64071,-0.029033,232.41
> view matrix models
> #38,-0.60566,-0.70889,0.36146,266.58,0.21101,0.29491,0.93193,105.92,-0.76724,0.64071,-0.029033,230.06
> view matrix models
> #38,-0.72224,-0.67174,0.16473,286.05,0.065572,0.1706,0.98316,133.05,-0.68853,0.72087,-0.079168,215.16
> view matrix models
> #38,-0.47003,-0.67432,0.56953,241.2,0.17784,0.55967,0.80941,102.54,-0.86455,0.48173,-0.14315,252.98
> view matrix models
> #38,-0.47003,-0.67432,0.56953,249.14,0.17784,0.55967,0.80941,98.999,-0.86455,0.48173,-0.14315,251.53
> view matrix models
> #38,-0.59825,-0.70633,0.37841,273.04,0.21367,0.31452,0.92489,101.29,-0.77229,0.63417,-0.037243,229.77
> fitmap #38 inMap #64
Fit molecule 9hud (#38) to map cryosparc_P483_J137_003_volume_map.mrc z flip
(#64) using 6282 atoms
average map value = 0.03512, steps = 80
shifted from previous position = 5.4
rotated from previous position = 3.39 degrees
atoms outside contour = 3664, contour level = 0.036179
Position of 9hud (#38) relative to cryosparc_P483_J137_003_volume_map.mrc z
flip (#64) coordinates:
Matrix rotation and translation
-0.63147092 -0.69242738 0.34898254 278.13803163
0.16768307 0.31747267 0.93332391 107.28593241
-0.75705144 0.64788536 -0.08436641 232.43243148
Axis -0.19962317 0.77351156 0.60152345
Axis point 188.76264795 0.00000000 -10.22905426
Rotation angle (degrees) 134.36143880
Shift along axis 167.27766991
> fitmap #38 inMap #64
Fit molecule 9hud (#38) to map cryosparc_P483_J137_003_volume_map.mrc z flip
(#64) using 6282 atoms
average map value = 0.03512, steps = 40
shifted from previous position = 0.0099
rotated from previous position = 0.0115 degrees
atoms outside contour = 3662, contour level = 0.036179
Position of 9hud (#38) relative to cryosparc_P483_J137_003_volume_map.mrc z
flip (#64) coordinates:
Matrix rotation and translation
-0.63136485 -0.69247722 0.34907556 278.12932035
0.16783951 0.31744825 0.93330409 107.26947039
-0.75710524 0.64784406 -0.08420063 232.43949274
Axis -0.19960443 0.77348336 0.60156592
Axis point 188.76447494 0.00000000 -10.24425096
Rotation angle (degrees) 134.35152473
Shift along axis 167.28298509
> view matrix models
> #38,-0.63136,-0.69248,0.34908,274.79,0.16784,0.31745,0.9333,108.96,-0.75711,0.64784,-0.084201,230.09
> fitmap #38 inMap #64
Fit molecule 9hud (#38) to map cryosparc_P483_J137_003_volume_map.mrc z flip
(#64) using 6282 atoms
average map value = 0.03512, steps = 88
shifted from previous position = 4.42
rotated from previous position = 0.00894 degrees
atoms outside contour = 3663, contour level = 0.036179
Position of 9hud (#38) relative to cryosparc_P483_J137_003_volume_map.mrc z
flip (#64) coordinates:
Matrix rotation and translation
-0.63139892 -0.69244150 0.34908479 278.12602696
0.16773664 0.31755383 0.93328667 107.27376736
-0.75709963 0.64783049 -0.08435534 232.44361126
Axis -0.19961308 0.77352989 0.60150323
Axis point 188.76295474 0.00000000 -10.22421164
Rotation angle (degrees) 134.35485805
Shift along axis 167.27745334
> view matrix models
> #38,-0.64713,-0.6735,0.35724,279.79,0.16615,0.33274,0.92827,107.01,-0.74406,0.66006,-0.10342,230.15
> view matrix models
> #38,-0.64713,-0.6735,0.35724,276.58,0.16615,0.33274,0.92827,108.12,-0.74406,0.66006,-0.10342,229.13
> fitmap #38 inMap #64
Fit molecule 9hud (#38) to map cryosparc_P483_J137_003_volume_map.mrc z flip
(#64) using 6282 atoms
average map value = 0.03512, steps = 80
shifted from previous position = 3.52
rotated from previous position = 1.63 degrees
atoms outside contour = 3659, contour level = 0.036179
Position of 9hud (#38) relative to cryosparc_P483_J137_003_volume_map.mrc z
flip (#64) coordinates:
Matrix rotation and translation
-0.63138477 -0.69243824 0.34911684 278.12114525
0.16772204 0.31760740 0.93327106 107.27149167
-0.75711466 0.64780772 -0.08439532 232.44867407
Axis -0.19961431 0.77354815 0.60147934
Axis point 188.76284344 0.00000000 -10.21708948
Rotation angle (degrees) 134.35374707
Shift along axis 167.27577632
> hide #!64 models
> show #!60 models
> view matrix models
> #38,0.4887,0.003934,0.87244,67.696,-0.61017,-0.71321,0.345,277.22,0.6236,-0.70094,-0.34614,69.091
> view matrix models
> #38,0.4887,0.003934,0.87244,62.759,-0.61017,-0.71321,0.345,271.12,0.6236,-0.70094,-0.34614,59.706
> view matrix models
> #38,0.4887,0.003934,0.87244,62.878,-0.61017,-0.71321,0.345,270.83,0.6236,-0.70094,-0.34614,60.391
> select subtract #38
Nothing selected
> hide #!38 models
> show #!38 models
> open /Users/amy/Downloads/cryosparc_P483_J136_004_volume_map.mrc
Opened cryosparc_P483_J136_004_volume_map.mrc as #65, grid size 400,400,400,
pixel 0.723, shown at level 0.00461, step 2, values float32
> hide #!60 models
> hide #!38 models
> surface dust #65 size 7.23
> volume #65 level 0.02522
> transparency #65 50
> volume flip #65 axis z
Opened cryosparc_P483_J136_004_volume_map.mrc z flip as #66, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> show #!38 models
> fitmap #38 inMap #66
Fit molecule 9hud (#38) to map cryosparc_P483_J136_004_volume_map.mrc z flip
(#66) using 6282 atoms
average map value = 0.05359, steps = 80
shifted from previous position = 1.58
rotated from previous position = 4.51 degrees
atoms outside contour = 1373, contour level = 0.025222
Position of 9hud (#38) relative to cryosparc_P483_J136_004_volume_map.mrc z
flip (#66) coordinates:
Matrix rotation and translation
0.49152778 0.08078197 0.86710711 58.94196264
-0.57115257 -0.72173556 0.39100196 263.45649346
0.65740794 -0.68743877 -0.30861424 55.13461431
Axis -0.84417530 0.16414704 -0.51031737
Axis point 0.00000000 145.46690985 -47.79590518
Rotation angle (degrees) 140.30102750
Shift along axis -34.64789549
> mmaker #37 to #38
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 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
score = 1674.4
RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
0.519)
> show #!37 models
> show #7 models
> mmaker #7 to #37
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 1ezx, chain C (#37) with 5a0c, chain A (#7), sequence alignment
score = 241.2
RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
3.073)
> hide #!37 models
> show #!37 models
> hide #!38 models
> show #!38 models
> hide #!37 models
> show #!37 models
> hide #!38 models
> hide #7 models
> volume #65 level 0.03378
> volume #66 level 0.03927
> volume #66 level 0.03004
> hide #!37 models
> volume gaussian #65 sDev 2
Opened cryosparc_P483_J136_004_volume_map.mrc gaussian as #67, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> ui tool show "Segment Map"
Segmenting cryosparc_P483_J136_004_volume_map.mrc gaussian, density threshold
0.002595
Only showing 60 of 69 regions.
Showing 60 of 69 region surfaces
165 watershed regions, grouped to 69 regions
Showing cryosparc_P483_J136_004_volume_map gaussian.seg - 69 regions, 60
surfaces
> select #68.13
1 model selected
> select add #68.6
2 models selected
> select add #68.23
3 models selected
> select add #68.24
4 models selected
> select add #68.29
5 models selected
> select add #68.20
6 models selected
> select add #68.5
7 models selected
> select add #68.37
8 models selected
> select add #68.33
9 models selected
> select add #68.11
10 models selected
> select add #68.26
11 models selected
> select add #68.14
12 models selected
> select add #68.7
13 models selected
> select add #68.3
14 models selected
> select add #68.19
15 models selected
> select add #68.8
16 models selected
> select add #68.35
17 models selected
> select add #68.28
18 models selected
> select add #68.12
19 models selected
> select add #68.15
20 models selected
> select add #68.4
21 models selected
> select add #68.40
22 models selected
> select add #68.36
23 models selected
> select add #68.48
24 models selected
> select add #68.51
25 models selected
> select add #68.53
26 models selected
> select add #68.59
27 models selected
> select add #68.58
28 models selected
> select add #68.57
29 models selected
> select add #68.54
30 models selected
> select add #68.16
31 models selected
> select add #68.44
32 models selected
> select add #68.25
33 models selected
> select add #68.50
34 models selected
> select add #68.31
35 models selected
> hide #!67 models
> select add #68.45
36 models selected
> select add #68.38
37 models selected
> select add #68.17
38 models selected
> select add #68.34
39 models selected
> select add #68.52
40 models selected
> select add #68.30
41 models selected
> select add #68.27
42 models selected
> select add #68.49
43 models selected
> select add #68.46
44 models selected
> select add #68.43
45 models selected
> select add #68.39
46 models selected
> select add #68.41
47 models selected
> select add #68.56
48 models selected
> select add #68.55
49 models selected
> show #!67 models
> show #!66 models
> hide #!66 models
> hide #!68 models
> show #!68 models
> hide #!68 models
> show #!66 models
> show #!68 models
> hide #!67 models
> hide #!66 models
> show #!65 models
> select add #68.42
50 models selected
> hide #!65 models
> select add #68.21
51 models selected
> show #!66 models
> hide #!66 models
> show #!65 models
> hide #!68 models
> show #!68 models
> hide #!68 models
> show #!68 models
> select add #68.47
52 models selected
> select add #68.10
53 models selected
> select subtract #68.10
52 models selected
> select add #68.60
53 models selected
> select add #68.1
54 models selected
> select subtract #68.1
53 models selected
> select add #68.1
54 models selected
> select subtract #68.1
53 models selected
> select #68.1
1 model selected
Segmenting cryosparc_P483_J136_004_volume_map.mrc gaussian, density threshold
0.002595
Only showing 60 of 69 regions.
Showing 60 of 69 region surfaces
165 watershed regions, grouped to 69 regions
Showing cryosparc_P483_J136_004_volume_map gaussian.seg - 69 regions, 60
surfaces
> close #68
> show #!67 models
> hide #!67 models
> volume #65 level 0.009704
> ui mousemode right "map eraser"
> volume erase #65 center 171.23,100.86,184.61 radius 29.508
Opened cryosparc_P483_J136_004_volume_map.mrc copy as #69, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> volume erase #69 center 84.398,121.62,173.8 radius 29.498
> surface dust #69 size 7.23
> volume #69 level 0.01365
> volume #69 level 0.01523
> ui mousemode right "translate selected models"
> volume gaussian #65 sDev 2
Opened cryosparc_P483_J136_004_volume_map.mrc gaussian as #68, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> ui mousemode right "map eraser"
Can only have one displayed volume when erasing
> hide #!69 models
> show #!69 models
> hide #!69 models
> hide #!68 models
> show #!68 models
> volume erase #68 center 199.87,114.16,177.51 radius 29.932
> volume erase #68 center 223.51,161,191.94 radius 29.932
> volume erase #68 center 230.79,129.47,140.96 radius 29.932
> volume erase #68 center 137.16,147.6,54.19 radius 29.932
> volume erase #68 center 74.443,93.395,201.66 radius 29.932
> volume erase #68 center 60.662,109.56,169.96 radius 29.932
> volume erase #68 center 81.784,129.86,147.37 radius 29.932
> volume erase #68 center 97.833,142.74,184.92 radius 14.894
> volume erase #68 center 93.234,158.27,115.41 radius 14.894
> volume erase #68 center 110.51,164.91,187.37 radius 14.894
> volume erase #68 center 126.3,181.61,190.42 radius 14.894
> volume erase #68 center 190.02,108.44,206.29 radius 14.894
> volume erase #68 center 212,136.35,210.5 radius 14.894
> volume erase #68 center 66.419,147.34,177.91 radius 14.894
> volume erase #68 center 94.954,148.62,156.51 radius 14.894
> volume erase #68 center 105.75,136.11,158.02 radius 14.894
> volume erase #68 center 169.12,113.8,156.36 radius 12.58
> volume erase #68 center 179.1,115.64,198.32 radius 12.58
> show #!65 models
> hide #!68 models
> volume #65 level 0.01773
> show #!68 models
Can only have one displayed volume when erasing
> hide #!65 models
> hide #!68 models
> show #!65 models
> hide #!65 models
> show #!68 models
> volume erase #68 center 173.45,108.86,188.42 radius 22.124
> volume erase #68 center 161.71,101.56,178.92 radius 22.124
> undo
[Repeated 1 time(s)]
> show #!68 models
> hide #!65 models
> volume erase #68 center 92.336,122.06,161.51 radius 22.124
Segmenting cryosparc_P483_J136_004_volume_map.mrc gaussian, density threshold
0.002595
Showing 50 region surfaces
124 watershed regions, grouped to 50 regions
Showing cryosparc_P483_J136_004_volume_map gaussian.seg - 50 regions, 50
surfaces
> select add #70.10
1 model selected
> select add #70.31
2 models selected
> select add #70.6
3 models selected
> select add #70.12
4 models selected
> select add #70.23
5 models selected
> select add #70.22
6 models selected
Drag select of 173, 7505 of 52828 triangles, 177, 26288 of 45472 triangles,
172, 156, 176, 25800 of 38068 triangles, 157, 17988 of 30408 triangles, 167,
152, 142, 6687 of 22324 triangles, 163, 64, 17140 of 19708 triangles, 12, 178,
169, 568 of 17388 triangles, 5, 143, 6044 of 15344 triangles, 144, 148, 135,
30, 12770 of 12984 triangles, 8, 52, 4331 of 12948 triangles, 125, 11085 of
12828 triangles, 6, 68, 5141 of 9284 triangles, 33, 35, 6919 of 6948
triangles, 68 cryosparc_P483_J136_004_volume_map.mrc gaussian
Drag select of 177, 8907 of 45472 triangles, 172, 35825 of 37284 triangles,
156, 176, 5888 of 38068 triangles, 157, 7846 of 30408 triangles, 167, 152,
7570 of 25900 triangles, 163, 12, 17106 of 17656 triangles, 178, 5, 144, 148,
13560 of 13800 triangles, 135, 12555 of 14540 triangles, 30, 6391 of 12984
triangles, 8, 125, 1329 of 12828 triangles, 6, 33, 3490 of 7340 triangles, 35,
1963 of 6948 triangles, 68 cryosparc_P483_J136_004_volume_map.mrc gaussian
> hide #!68 models
Drag select of 177, 10859 of 45472 triangles, 172, 176, 10027 of 38068
triangles, 149, 177 of 29032 triangles, 152, 12625 of 25900 triangles, 163, 5,
144, 135, 14423 of 14540 triangles, 30, 11045 of 12984 triangles, 8, 125, 2434
of 12828 triangles, 6, 33, 6568 of 7340 triangles, 35, 5541 of 6948 triangles
> close #70
> show #!66 models
> hide #!66 models
> show #!65 models
> show #!68 models
> close #68-69
> close #67
> volume gaussian #65 sDev 2
Opened cryosparc_P483_J136_004_volume_map.mrc gaussian as #67, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> open /Users/amy/Downloads/cryosparc_P371_J1247_003_volume_map.mrc
Opened cryosparc_P371_J1247_003_volume_map.mrc as #68, grid size 300,300,300,
pixel 0.867, shown at level 0.0217, step 2, values float32
> hide #!67 models
> volume #68 level 0.07077
> show #!8 models
> transparenct #68 50
Unknown command: transparenct #68 50
> transparency #68 50
> fitmap #8 inMap #68
Fit molecule 1ezx (#8) to map cryosparc_P371_J1247_003_volume_map.mrc (#68)
using 3984 atoms
average map value = 0.0799, steps = 64
shifted from previous position = 1.9
rotated from previous position = 5.61 degrees
atoms outside contour = 1925, contour level = 0.07077
Position of 1ezx (#8) relative to cryosparc_P371_J1247_003_volume_map.mrc
(#68) coordinates:
Matrix rotation and translation
-0.34797185 0.02707514 -0.93711394 206.68051797
0.14066384 -0.98675962 -0.08074121 177.03298135
-0.92689227 -0.15991372 0.33955607 198.02271581
Axis -0.57026324 -0.07362457 0.81815601
Axis point 168.54386706 102.19253410 0.00000000
Rotation angle (degrees) 176.01946831
Shift along axis 31.11719577
> show #!57 models
> select add #57
1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 3 models selected
> mmaker #57 to #8
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 1ezx, chain C (#8) with copy of 1ezx, chain C (#57), sequence
alignment score = 1096
RMSD between 140 pruned atom pairs is 0.000 angstroms; (across all 140 pairs:
0.000)
> select subtract #57
Nothing selected
> select add #57
1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 3 models selected
> hide #!8 models
> show #!8 models
> ui mousemode right "translate selected models"
> view matrix models
> #57,-0.55581,-0.066238,-0.82867,220.13,0.27617,-0.95492,-0.10891,166.76,-0.7841,-0.28938,0.54905,178.74
> view matrix models
> #57,-0.44814,0.013112,-0.89387,212.91,0.19695,-0.97388,-0.11303,173.83,-0.872,-0.2267,0.43385,190.3
> view matrix models
> #57,-0.44814,0.013112,-0.89387,212.84,0.19695,-0.97388,-0.11303,176.3,-0.872,-0.2267,0.43385,191.28
> view matrix models
> #57,-0.70986,-0.70171,-0.060879,208.01,0.69037,-0.67603,-0.25765,136.82,0.13964,-0.22492,0.96432,82.152
> view matrix models
> #57,-0.70986,-0.70171,-0.060879,209.15,0.69037,-0.67603,-0.25765,137.83,0.13964,-0.22492,0.96432,86.098
> view matrix models
> #57,-0.52828,-0.77583,-0.34499,210.69,0.84041,-0.53567,-0.082284,113.45,-0.12096,-0.3334,0.93499,111.22
> fitmap #57 inMap #68
Fit molecule copy of 1ezx (#57) to map cryosparc_P371_J1247_003_volume_map.mrc
(#68) using 1009 atoms
average map value = 0.05715, steps = 92
shifted from previous position = 1.85
rotated from previous position = 22.4 degrees
atoms outside contour = 740, contour level = 0.07077
Position of copy of 1ezx (#57) relative to
cryosparc_P371_J1247_003_volume_map.mrc (#68) coordinates:
Matrix rotation and translation
-0.60074737 -0.69741151 -0.39079378 215.40326299
0.67365936 -0.70482938 0.22225799 115.60603445
-0.43044821 -0.12974098 0.89324219 133.98043752
Axis -0.24857103 0.02800277 0.96820880
Axis point 100.60140928 106.25888332 0.00000000
Rotation angle (degrees) 134.92392438
Shift along axis 79.41531641
> hide #!8 models
> view matrix models
> #57,-0.55549,-0.80836,-0.19489,204.29,0.77301,-0.58839,0.23717,104.09,-0.30639,-0.018907,0.95172,118.37
> view matrix models
> #57,-0.55549,-0.80836,-0.19489,206,0.77301,-0.58839,0.23717,104.98,-0.30639,-0.018907,0.95172,120.21
> view matrix models
> #57,-0.33676,-0.93674,0.09544,176.41,0.94008,-0.34023,-0.022246,98.96,0.05331,0.08223,0.99519,86.499
> view matrix models
> #57,-0.33676,-0.93674,0.09544,176.42,0.94008,-0.34023,-0.022246,99.819,0.05331,0.08223,0.99519,85.597
> view matrix models
> #57,-0.11119,-0.60614,-0.78754,195.64,0.65285,-0.64203,0.40198,108.39,-0.74928,-0.46945,0.46711,190.42
> view matrix models
> #57,0.78168,0.24914,-0.57175,92.445,0.18825,-0.96824,-0.16454,182.56,-0.59459,0.020991,-0.80376,231.51
> view matrix models
> #57,0.51703,0.78986,-0.32985,88.973,0.65853,-0.61323,-0.43621,150.13,-0.54682,0.0083211,-0.83721,229.65
> view matrix models
> #57,0.51703,0.78986,-0.32985,91.831,0.65853,-0.61323,-0.43621,150.09,-0.54682,0.0083211,-0.83721,234.12
> view matrix models
> #57,0.55299,0.36331,-0.7498,120.29,0.22263,-0.93163,-0.28721,185.16,-0.80289,-0.0081052,-0.59607,242.91
> view matrix models
> #57,0.55299,0.36331,-0.7498,118.48,0.22263,-0.93163,-0.28721,185.69,-0.80289,-0.0081052,-0.59607,239.55
> view matrix models
> #57,0.92569,-0.35496,0.13079,59.902,0.0091285,-0.32469,-0.94578,222.6,0.37818,0.87669,-0.29732,108.08
> view matrix models
> #57,-0.3165,-0.83947,0.44172,155.86,0.42443,-0.54177,-0.7255,182.72,0.84834,-0.042141,0.52777,49.092
> view matrix models
> #57,-0.3165,-0.83947,0.44172,156.19,0.42443,-0.54177,-0.7255,182.46,0.84834,-0.042141,0.52777,49.883
> view matrix models
> #57,0.040165,-0.95688,0.2877,137.9,0.92992,-0.069542,-0.36112,111.92,0.36556,0.28204,0.88703,63.1
> view matrix models
> #57,0.040165,-0.95688,0.2877,138.99,0.92992,-0.069542,-0.36112,111.84,0.36556,0.28204,0.88703,64.867
> view matrix models
> #57,0.18721,-0.98102,0.050423,139.78,0.96897,0.17599,-0.17355,93.385,0.16139,0.081349,0.98353,81.124
> mmaker #7 to #8
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 1ezx, chain C (#8) with 5a0c, chain A (#7), sequence alignment
score = 241.2
RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
3.073)
> select add #7
2892 atoms, 2759 bonds, 5 pseudobonds, 549 residues, 4 models selected
> show #7 models
> select subtract #57
1883 atoms, 1745 bonds, 394 residues, 1 model selected
> hide #!57 models
> select #7/A
1883 atoms, 1745 bonds, 394 residues, 1 model selected
> select subtract #7
Nothing selected
> select #7/A
1883 atoms, 1745 bonds, 394 residues, 1 model selected
> select #7/A: 202
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #7/A: 202
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 6 atom styles
> rainbow sel
> select add #7
1883 atoms, 1745 bonds, 394 residues, 1 model selected
> select subtract #7
Nothing selected
> show #!37 models
> hide #!37 models
> show #!8 models
> hide #!8 models
> open /Users/amy/Downloads/cryosparc_P371_J1248_004_volume_map.mrc
Opened cryosparc_P371_J1248_004_volume_map.mrc as #69, grid size 300,300,300,
pixel 0.867, shown at level 0.0367, step 2, values float32
> volume #69 level 0.08383
> hide #!68 models
> volume #69 level 0.0762
> transparency #69 50
> hide #7 models
> close #50-56
> close #43-48
> show #!65 models
> volume gaussian #65 sDev 2
Opened cryosparc_P483_J136_004_volume_map.mrc gaussian as #43, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> ui mousemode right "map eraser"
> volume erase #43 center 75.013,107.83,176.28 radius 23.833
> volume erase #43 center 194.75,109.99,182.34 radius 28.983
> volume erase #43 center 224.93,121.74,145.38 radius 28.983
> volume erase #43 center 210.7,158.2,175.15 radius 28.983
> volume erase #43 center 208.21,147.09,205.7 radius 28.983
> volume erase #43 center 188.54,118.48,207.86 radius 28.983
> volume erase #43 center 76.857,145.76,159.87 radius 28.983
> volume erase #43 center 87.79,161.6,111.25 radius 28.983
> volume erase #43 center 126.19,148.22,60.086 radius 28.983
> surface dust #43 size 7.23
[Repeated 2 time(s)]
> volume erase #43 center 98.252,123.11,133.43 radius 28.983
> ui mousemode right "translate selected models"
> hide #!43 models
> show #!43 models
Segmenting cryosparc_P483_J136_004_volume_map.mrc gaussian, density threshold
0.002595
Showing 54 region surfaces
134 watershed regions, grouped to 54 regions
Showing cryosparc_P483_J136_004_volume_map gaussian.seg - 54 regions, 54
surfaces
Drag select of 180, 4556 of 45584 triangles, 187, 31245 of 37284 triangles,
177, 33991 of 34540 triangles, 179, 626 of 37968 triangles, 170, 1849 of 30408
triangles, 183, 146, 4014 of 25900 triangles, 166, 12, 182, 5, 151, 157, 9644
of 13800 triangles, 160, 7260 of 14540 triangles, 30, 3371 of 12984 triangles,
8, 6, 33, 892 of 7340 triangles, 35, 143 of 6948 triangles, 43
cryosparc_P483_J136_004_volume_map.mrc gaussian
Drag select of 189, 15171 of 45152 triangles, 144, 28176 of 29416 triangles,
186, 153, 26060 of 29032 triangles, 165, 16225 of 23204 triangles, 171, 20862
of 21324 triangles, 181, 612 of 19816 triangles, 188, 9417 of 18732 triangles,
184, 11190 of 17388 triangles, 69, 12493 of 16160 triangles, 83, 159, 3373 of
15344 triangles, 100, 109, 4788 of 13396 triangles, 54, 54 of 12948 triangles,
190, 3956 of 13608 triangles, 148, 93 of 11564 triangles, 167, 713 of 12312
triangles, 136, 1067 of 12828 triangles, 95, 7439 of 9752 triangles, 82, 43
cryosparc_P483_J136_004_volume_map.mrc gaussian
> hide #!43 models
> show #!43 models
> select add #44.51
41 models selected
> select add #44.53
42 models selected
> hide #!43 models
> select add #44.10
43 models selected
Ungrouped to 64 regions, but did not show all surfaces, see Options
> select clear
> select #44.62
1 model selected
> select #44.21
1 model selected
Ungrouped to 2 regions, but did not show their surfaces, see Options
Smoothing and grouping, standard deviation 5 voxels
Showing 28 region surfaces
Got 28 regions after smoothing 5 voxels.
Ungrouped to 86 regions, but did not show all surfaces, see Options
Drag select of 134
[Repeated 1 time(s)]
> select clear
> select #44.72
1 model selected
> select clear
> select #44.73
1 model selected
> select add #44.74
2 models selected
> show #!43 models
> hide #!44 models
> volume #43 level 0.01177
> ui mousemode right "map eraser"
> volume erase #43 center 170.19,107.1,177.93 radius 16.889
> ui mousemode right "translate selected models"
> close #44
> volume gaussian #65 sDev 2
Opened cryosparc_P483_J136_004_volume_map.mrc gaussian as #44, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> close #44
Segmenting cryosparc_P483_J136_004_volume_map.mrc gaussian, density threshold
0.011767
Showing 49 region surfaces
113 watershed regions, grouped to 49 regions
Showing cryosparc_P483_J136_004_volume_map gaussian.seg - 49 regions, 49
surfaces
> hide #!43 models
Drag select of 152, 22015 of 40248 triangles, 160, 137, 162, 19815 of 27632
triangles, 145, 22686 of 24068 triangles, 154, 132, 19102 of 20860 triangles,
149, 128, 343 of 19360 triangles, 12, 157, 151, 5666 of 14648 triangles, 155,
15 of 14140 triangles, 121, 8147 of 14452 triangles, 126, 124, 5, 50, 4342 of
11924 triangles, 6, 133, 26, 116, 11741 of 11768 triangles, 7, 32, 34
Drag select of 159, 9755 of 37648 triangles, 125, 24182 of 24328 triangles,
158, 18998 of 22744 triangles, 139, 10853 of 19468 triangles, 142, 17469 of
19372 triangles, 128, 5249 of 19360 triangles, 63, 3508 of 13216 triangles,
82, 11209 of 11804 triangles, 90, 161, 1720 of 12188 triangles, 84, 4555 of
9228 triangles, 71, 6615 of 6864 triangles
Drag select of 128, 163, 7108 of 17660 triangles, 94, 10211 of 10636
triangles, 123, 7213 of 10336 triangles, 146, 6495 of 11584 triangles, 88,
3550 of 8592 triangles
Showing 49 region surfaces
> select #44.46
1 model selected
> show #!43 models
> hide #!43 models
> select #44.13
1 model selected
> select #44.13
1 model selected
> select #44.3
1 model selected
> select #44.3
1 model selected
Ungrouped to 2 regions
> select #44.13
1 model selected
Ungrouped to 2 regions
> select #44.3
1 model selected
Ungrouped to 2 regions
> select #44.51
1 model selected
Ungrouped to 2 regions
> select #44.54
1 model selected
Ungrouped to 2 regions
> show #!43 models
> hide #!43 models
> show #!43 models
> hide #!43 models
> show #!43 models
> hide #!43 models
> select #44.55
1 model selected
> select #44.55
1 model selected
> select clear
Please select one ore more regions to save to .mrc file
Drag select of 156, 138, 61, 127, 65, 93, 87, 92, 76, 68, 79, 69
Saving 12 regions to mrc file...
Opened base_cryosparc_P483_J136_004_volume_map_12_regions.mrc as #45, grid
size 75,64,70, pixel 0.723, shown at step 1, values float32
Wrote base_cryosparc_P483_J136_004_volume_map_12_regions.mrc
> volume #45 level 0.01277
> hide #!44 models
> show #!44 models
Deleted 12 regions
Showing 42 region surfaces
> hide #!45 models
> show #!45 models
> hide #!45 models
Drag select of 152, 159, 160, 137, 162, 125, 158, 145, 154, 139, 132, 142,
149, 128, 163, 12, 157, 151, 155, 121, 126, 63, 82, 124, 5, 50, 6, 133, 90,
26, 161, 94, 116, 123, 146, 7, 84, 88, 74, 71, 32, 34
Saving 42 regions to mrc file...
Opened substract_cryosparc_P483_J136_004_volume_map_42_regions.mrc as #46,
grid size 90,89,178, pixel 0.723, shown at step 1, values float32
Wrote substract_cryosparc_P483_J136_004_volume_map_42_regions.mrc
> select add #44
43 models selected
> select subtract #44
Nothing selected
> hide #!44 models
> volume #46 level 0.01896
> show #!44 models
> hide #!44 models
> show #!45 models
> volume resample #45 onGrid #65
Opened base_cryosparc_P483_J136_004_volume_map_12_regions.mrc resampled as
#47, grid size 400,400,400, pixel 0.723, shown at step 1, values float32
> show #!45 models
> hide #!45 models
> volume resample #46 onGrid #65
Opened substract_cryosparc_P483_J136_004_volume_map_42_regions.mrc resampled
as #48, grid size 400,400,400, pixel 0.723, shown at step 1, values float32
> hide #!48 models
> show #!48 models
> save "/Users/amy/Desktop/SPA AAT_HNE/9C5_Fab_AAT_HNE/For mask
> generation/Base_mask_J136.mrc" models #47
> save "/Users/amy/Desktop/SPA AAT_HNE/9C5_Fab_AAT_HNE/For mask
> generation/Substract_mask_J136.mrc" models #48
> hide #!48 models
> hide #!47 models
> show #!66 models
> volume #66 level 0.01465
> hide #!66 models
> show #!66 models
> show #!65 models
> hide #!66 models
> hide #!65 models
> show #!66 models
> volume #66 level 0.0762
> volume #66 level 0.05963
> open /Users/amy/Downloads/Position_4_4_stack_Vol.mrc
Opened Position_4_4_stack_Vol.mrc as #50, grid size 1024,1024,200, pixel
6.2,6.2,6.2, shown at level 0.00197, step 4, values float32
> open /Users/amy/Downloads/cryosparc_P483_J163_009_volume_map.mrc
Opened cryosparc_P483_J163_009_volume_map.mrc as #51, grid size 400,400,400,
pixel 0.723, shown at level 0.00345, step 2, values float32
> hide #!50 models
> hide #!66 models
> close #50
> volume #51 level 0.01856
> transparency #51 50
> show #!38 models
> select add #38
6282 atoms, 6138 bonds, 1077 residues, 1 model selected
> volume flip #51 axis z
Opened cryosparc_P483_J163_009_volume_map.mrc z flip as #50, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> fitmap #38 inMap #50
Fit molecule 9hud (#38) to map cryosparc_P483_J163_009_volume_map.mrc z flip
(#50) using 6282 atoms
average map value = 0.07848, steps = 68
shifted from previous position = 0.869
rotated from previous position = 1.21 degrees
atoms outside contour = 1202, contour level = 0.018564
Position of 9hud (#38) relative to cryosparc_P483_J163_009_volume_map.mrc z
flip (#50) coordinates:
Matrix rotation and translation
0.47930263 0.06820977 0.87499511 60.65156876
-0.57459125 -0.72922061 0.37159415 263.89520826
0.66341081 -0.68087058 -0.31032461 53.93040141
Axis -0.84112622 0.16909745 -0.51372438
Axis point 0.00000000 145.65173307 -47.89349763
Rotation angle (degrees) 141.27168221
Shift along axis -34.09698023
> select subtract #38
Nothing selected
> show #!37 models
> mmaker #37 to #38
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 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
score = 1674.4
RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
0.519)
> hide #!37 models
> hide #!38 models
> show #!37 models
> ui mousemode right "tape measure"
> marker segment #52 position 174.9,170.7,80.95 toPosition 149.1,120.4,104.7
> color yellow radius 0.1807 label 61.39 labelHeight 6.139 labelColor yellow
> marker segment #52 position 173.6,172.2,80.09 toPosition 131.7,129.6,94.55
> color yellow radius 0.1807 label 61.46 labelHeight 6.146 labelColor yellow
> marker segment #52 position 168.9,170.1,79.92 toPosition 119.6,140.5,107.7
> color yellow radius 0.1807 label 63.85 labelHeight 6.385 labelColor yellow
> marker segment #52 position 162.3,169.9,78.45 toPosition 131.8,125.9,101.6
> color yellow radius 0.1807 label 58.29 labelHeight 5.829 labelColor yellow
> close #52
> open /Users/amy/Downloads/cryosparc_P483_J166_007_volume_map.mrc
Opened cryosparc_P483_J166_007_volume_map.mrc as #52, grid size 400,400,400,
pixel 0.723, shown at level 0.00871, step 2, values float32
> volume #52 level 0.03218
> volume flip #52 50
Expected a keyword
> volume flip #52 axis z
Opened cryosparc_P483_J166_007_volume_map.mrc z flip as #53, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> transparency #53 50
> fitmap #38 inMap #53
Fit molecule 9hud (#38) to map cryosparc_P483_J166_007_volume_map.mrc z flip
(#53) using 6282 atoms
average map value = 0.0755, steps = 88
shifted from previous position = 0.675
rotated from previous position = 2.29 degrees
atoms outside contour = 1730, contour level = 0.032179
Position of 9hud (#38) relative to cryosparc_P483_J166_007_volume_map.mrc z
flip (#53) coordinates:
Matrix rotation and translation
0.48708054 0.10074896 0.86752649 58.26714282
-0.57324776 -0.71251935 0.40460253 263.40109171
0.65889268 -0.69438163 -0.28930019 55.22725475
Axis -0.84150595 0.15975352 -0.51608774
Axis point 0.00000000 145.38448995 -49.65713741
Rotation angle (degrees) 139.23284387
Shift along axis -35.45500404
> show #!38 models
> mmaker #37 to #38
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 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
score = 1674.4
RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
0.519)
> hide #!38 models
> show #7 models
> mmaker #7 to #37
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 1ezx, chain C (#37) with 5a0c, chain A (#7), sequence alignment
score = 241.2
RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
3.073)
> hide #!37 models
> volume #53 level 0.09551
> volume #53 level 0.05065
> volume #53 level 0.04273
> hide #7 models
> open /Users/amy/Downloads/cryosparc_P483_J178_007_volume_map.mrc
Opened cryosparc_P483_J178_007_volume_map.mrc as #54, grid size 400,400,400,
pixel 0.723, shown at level 0.00984, step 2, values float32
> volume #54 level 0.02797
> volume flip #54 axis z
Opened cryosparc_P483_J178_007_volume_map.mrc z flip as #55, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> transparency #55 50
> show #7 models
> hide #7 models
> show #7 models
> select add #7
1883 atoms, 1745 bonds, 394 residues, 1 model selected
> select subtract #7
Nothing selected
> hide #7 models
> show #!8 models
> select add #8
3984 atoms, 3982 bonds, 5 pseudobonds, 592 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.74339,-0.4472,0.49738,176.11,0.56886,-0.81386,0.11846,127.4,0.35182,0.371,0.85941,53.336
> view matrix models
> #8,0.38457,0.070001,0.92044,48.03,0.66601,-0.71147,-0.22416,135.06,0.63917,0.69922,-0.32023,84.211
> view matrix models
> #8,0.38457,0.070001,0.92044,48.132,0.66601,-0.71147,-0.22416,145.94,0.63917,0.69922,-0.32023,107.63
> view matrix models
> #8,-0.11357,-0.011929,0.99346,82.463,0.67784,-0.73199,0.068701,129.45,0.72638,0.68121,0.091219,79.052
> hide #!55 models
> show #!54 models
> transparency #54 50
> view matrix models
> #8,-0.11357,-0.011929,0.99346,88.184,0.67784,-0.73199,0.068701,128.28,0.72638,0.68121,0.091219,43.943
> view matrix models
> #8,0.98922,0.13889,-0.046321,63.821,0.14063,-0.98938,0.036662,180.17,-0.040737,-0.042781,-0.99825,195.61
> view matrix models
> #8,-0.22454,0.34562,-0.91111,186.4,0.4892,-0.76865,-0.41214,170.57,-0.84277,-0.53826,0.0035149,218.83
> view matrix models
> #8,-0.22454,0.34562,-0.91111,190.27,0.4892,-0.76865,-0.41214,172.31,-0.84277,-0.53826,0.0035149,198.32
> hide #!8 models
> select subtract #8
Nothing selected
> show #!38 models
> select add #38
6282 atoms, 6138 bonds, 1077 residues, 1 model selected
> view matrix models
> #38,0.58456,0.63428,-0.50594,39.545,0.32988,0.3839,0.86244,72.759,0.74126,-0.67105,0.015176,37.498
> view matrix models
> #38,-0.62989,-0.2889,-0.72095,269.75,0.43669,0.63589,-0.63635,64.932,0.64229,-0.71567,-0.27439,58.484
> view matrix models
> #38,-0.79758,-0.56471,-0.21208,300.49,0.093917,0.23104,-0.9684,138.83,0.59586,-0.79229,-0.13123,66.978
> view matrix models
> #38,-0.79758,-0.56471,-0.21208,298.65,0.093917,0.23104,-0.9684,128.19,0.59586,-0.79229,-0.13123,84.027
> view matrix models
> #38,-0.65099,-0.75245,0.1001,278.77,-0.2865,0.12144,-0.95035,192.34,0.70294,-0.64735,-0.29463,63.572
> view matrix models
> #38,-0.65099,-0.75245,0.1001,273.74,-0.2865,0.12144,-0.95035,188.77,0.70294,-0.64735,-0.29463,64.627
> hide #!54 models
> show #!55 models
> view matrix models
> #38,0.92945,0.36602,-0.046307,-17.327,-0.12262,0.18809,-0.97447,160.6,-0.34796,0.9114,0.2197,164.6
> view matrix models
> #38,0.68418,0.72711,0.05661,6.3245,-0.24646,0.30357,-0.92038,175.08,-0.6864,0.61576,0.3869,227.39
> view matrix models
> #38,0.68418,0.72711,0.05661,6.2981,-0.24646,0.30357,-0.92038,173.03,-0.6864,0.61576,0.3869,222.11
> fitmap #38 inMap #55
Fit molecule 9hud (#38) to map cryosparc_P483_J178_007_volume_map.mrc z flip
(#55) using 6282 atoms
average map value = 0.07095, steps = 260
shifted from previous position = 2.45
rotated from previous position = 40.2 degrees
atoms outside contour = 1485, contour level = 0.027968
Position of 9hud (#38) relative to cryosparc_P483_J178_007_volume_map.mrc z
flip (#55) coordinates:
Matrix rotation and translation
0.68744757 0.35641921 0.63275685 15.52206548
0.28938953 0.66468217 -0.68880429 73.81019326
-0.66608526 0.65663002 0.35379014 216.09676949
Axis 0.71899263 0.69409402 -0.03582029
Axis point 0.00000000 -189.86123076 144.51310834
Rotation angle (degrees) 69.33153492
Shift along axis 54.65081588
> mmaker #8 to #38
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 9hud, chain A (#38) with 1ezx, chain A (#8), sequence alignment
score = 1674.4
RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
0.519)
> hide #!38 models
> select subtract #38
Nothing selected
> show #!8 models
> mmaker #7 to #8
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 1ezx, chain C (#8) with 5a0c, chain A (#7), sequence alignment
score = 241.2
RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
3.073)
> hide #!8 models
> show #7 models
> volume #55 level 0.03303
> open /Users/amy/Downloads/cryosparc_P483_J178_007_volume_map.mrc
Opened cryosparc_P483_J178_007_volume_map.mrc as #56, grid size 400,400,400,
pixel 0.723, shown at level 0.00984, step 2, values float32
> volume #56 level 0.0196
> close #56
> open /Users/amy/Downloads/cryosparc_P483_J179_005_volume_map.mrc
Opened cryosparc_P483_J179_005_volume_map.mrc as #56, grid size 400,400,400,
pixel 0.723, shown at level 0.00903, step 2, values float32
> open /Users/amy/Downloads/cryosparc_P483_J180_002_volume_map.mrc
Opened cryosparc_P483_J180_002_volume_map.mrc as #70, grid size 400,400,400,
pixel 0.723, shown at level 0.00199, step 2, values float32
> hide #!70 models
> show #!66 models
> hide #!66 models
> show #!67 models
> open /Users/amy/Downloads/cryosparc_P483_J183_007_volume_map.mrc
Opened cryosparc_P483_J183_007_volume_map.mrc as #71, grid size 400,400,400,
pixel 0.723, shown at level 0.0116, step 2, values float32
> hide #!67 models
> volume #71 level 0.03377
> volume #71 level 0.03909
> transparency #71 50
> hide #7 models
> show #!38 models
> select add #38
6282 atoms, 6138 bonds, 1077 residues, 1 model selected
> view matrix models
> #38,-0.91266,0.065596,-0.40341,292.72,0.36322,0.5827,-0.727,65.755,0.18738,-0.81003,-0.55564,148.75
> view matrix models
> #38,-0.72502,-0.2597,-0.63788,278.46,0.38017,0.62139,-0.68509,61.067,0.57429,-0.73921,-0.3518,82.291
> view matrix models
> #38,-0.72502,-0.2597,-0.63788,277.14,0.38017,0.62139,-0.68509,52.977,0.57429,-0.73921,-0.3518,86.091
> view matrix models
> #38,-0.65947,-0.28553,-0.69539,268.48,0.35515,0.69696,-0.62299,53.205,0.66254,-0.65781,-0.35822,69.098
> view matrix models
> #38,-0.65947,-0.28553,-0.69539,267.26,0.35515,0.69696,-0.62299,52.554,0.66254,-0.65781,-0.35822,69.625
> close #58-69
> fitmap #38 inMap #71
Fit molecule 9hud (#38) to map cryosparc_P483_J183_007_volume_map.mrc (#71)
using 6282 atoms
average map value = 0.07544, steps = 148
shifted from previous position = 7.45
rotated from previous position = 12.1 degrees
atoms outside contour = 1976, contour level = 0.039086
Position of 9hud (#38) relative to cryosparc_P483_J183_007_volume_map.mrc
(#71) coordinates:
Matrix rotation and translation
-0.67498701 -0.41761657 -0.60826719 272.94445864
0.34716985 0.54767448 -0.76126592 67.90283128
0.65104966 -0.72501662 -0.22468927 71.15250272
Axis 0.02459578 -0.85446836 0.51892087
Axis point 117.22275735 0.00000000 126.50966305
Rotation angle (degrees) 132.53192375
Shift along axis -14.38502000
> mmaker #8 to #38
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 9hud, chain A (#38) with 1ezx, chain A (#8), sequence alignment
score = 1674.4
RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
0.519)
> show #!8 models
> select subtract #38
Nothing selected
> hide #!38 models
> show #7 models
> mmaker #7 to #8
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 1ezx, chain C (#8) with 5a0c, chain A (#7), sequence alignment
score = 241.2
RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
3.073)
> hide #!8 models
> open "/Users/amy/Downloads/cryosparc_P371_J1247_003_volume_map (1).mrc"
Opened cryosparc_P371_J1247_003_volume_map (1).mrc as #58, grid size
300,300,300, pixel 0.867, shown at level 0.0217, step 2, values float32
> hide #7 models
> volume #58 level 0.07127
> transparency 58 50
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency #58 50
> select add #58
2 models selected
> select subtract #58
Nothing selected
> show #!57 models
> hide #!57 models
> show #!37 models
> select add #37
3984 atoms, 3982 bonds, 5 pseudobonds, 592 residues, 3 models selected
> view matrix models
> #37,-0.92665,0.37309,0.046068,189.97,-0.3746,-0.92671,-0.029877,215.08,0.031544,-0.044943,0.99849,41.461
> view matrix models
> #37,-0.95684,-0.22555,-0.18327,235.41,0.22555,-0.974,0.021102,173.18,-0.18327,-0.021145,0.98284,55.964
> view matrix models
> #37,-0.95684,-0.22555,-0.18327,230.3,0.22555,-0.974,0.021102,164.37,-0.18327,-0.021145,0.98284,103.6
> view matrix models
> #37,-0.71551,-0.36432,-0.59609,244.23,0.27076,-0.93118,0.24412,146.37,-0.644,0.013275,0.76491,146.06
> view matrix models
> #37,-0.38059,-0.21113,-0.90032,230.74,0.23197,-0.96426,0.12806,157.34,-0.89517,-0.16011,0.41597,192.06
> view matrix models
> #37,-0.38059,-0.21113,-0.90032,226.85,0.23197,-0.96426,0.12806,158.76,-0.89517,-0.16011,0.41597,189.5
> fitmap #37 inMap #58
Fit molecule 1ezx (#37) to map cryosparc_P371_J1247_003_volume_map (1).mrc
(#58) using 3984 atoms
average map value = 0.0799, steps = 112
shifted from previous position = 8.44
rotated from previous position = 14 degrees
atoms outside contour = 1944, contour level = 0.071265
Position of 1ezx (#37) relative to cryosparc_P371_J1247_003_volume_map (1).mrc
(#58) coordinates:
Matrix rotation and translation
-0.34799611 0.02716421 -0.93710235 206.67239671
0.14052585 -0.98677538 -0.08078885 177.04596820
-0.92690409 -0.15980131 0.33957672 198.01665488
Axis -0.57025546 -0.07360376 0.81816330
Axis point 168.54356692 102.18640974 0.00000000
Rotation angle (degrees) 176.02747367
Shift along axis 31.12264873
> open "/Users/amy/Downloads/cryosparc_P371_J1247_003_volume_map (1).mrc"
Opened cryosparc_P371_J1247_003_volume_map (1).mrc as #59, grid size
300,300,300, pixel 0.867, shown at level 0.0217, step 2, values float32
> volume #59 level 0.06978
> hide #!58 models
> mmaker #7 to #37
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 1ezx, chain C (#37) with 5a0c, chain A (#7), sequence alignment
score = 241.2
RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
3.073)
> show #7 models
> hide #!59 models
> show #!58 models
> hide #!58 models
> show #!59 models
> transparency #59 50
> ui mousemode right "map eraser"
> hide #7 models
> hide #!37 models
> select subtract #37
Nothing selected
> volume erase #59 center 116.15,104.56,160.67 radius 47.97
Opened cryosparc_P371_J1247_003_volume_map (1).mrc copy as #61, grid size
300,300,300, pixel 0.867, shown at step 1, values float32
> volume erase #61 center 122.57,113.18,101.86 radius 47.97
> ui mousemode right "translate selected models"
> show #18 models
> select #18/A:202
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> rainbow sel
> select add #18
1883 atoms, 1745 bonds, 394 residues, 1 model selected
> select subtract #18
Nothing selected
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> hide #18 models
> show #7 models
> show #18 models
> mmaker #18 to #7
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 5a0c, chain A (#7) with copy of 5a0c, chain A (#18), sequence
alignment score = 1112.7
RMSD between 218 pruned atom pairs is 0.000 angstroms; (across all 218 pairs:
0.000)
> color #18 #ed91dfff
> color #18 #ebc5edff
> fitmap #7 inMap #59
Fit molecule 5a0c (#7) to map cryosparc_P371_J1247_003_volume_map (1).mrc
(#59) using 1883 atoms
average map value = 0.0522, steps = 120
shifted from previous position = 3.71
rotated from previous position = 23.2 degrees
atoms outside contour = 1476, contour level = 0.06978
Position of 5a0c (#7) relative to cryosparc_P371_J1247_003_volume_map (1).mrc
(#59) coordinates:
Matrix rotation and translation
-0.93248311 0.31677416 0.17357817 149.49808518
-0.24611565 -0.20545531 -0.94721444 169.75896469
-0.26439050 -0.92598178 0.26954669 154.83015425
Axis 0.02975759 0.61381323 -0.78889024
Axis point 98.48308815 127.59008236 0.00000000
Rotation angle (degrees) 159.09861794
Shift along axis -13.49499578
> hide #18 models
> ui mousemode right "map eraser"
> volume erase #61 center 140.38,143.93,165.02 radius 9.1821
> volume erase #61 center 135.35,144.22,156.8 radius 9.1821
> volume erase #61 center 126.68,146.69,162.17 radius 9.1821
> ui mousemode right "translate selected models"
> fitmap #7 inMap #59
Fit molecule 5a0c (#7) to map cryosparc_P371_J1247_003_volume_map (1).mrc
(#59) using 1883 atoms
average map value = 0.0522, steps = 48
shifted from previous position = 0.00729
rotated from previous position = 0.02 degrees
atoms outside contour = 1476, contour level = 0.06978
Position of 5a0c (#7) relative to cryosparc_P371_J1247_003_volume_map (1).mrc
(#59) coordinates:
Matrix rotation and translation
-0.93245587 0.31693119 0.17343780 149.49596389
-0.24610156 -0.20574256 -0.94715575 169.75337215
-0.26449966 -0.92586426 0.26984311 154.82942667
Axis 0.02983605 0.61368746 -0.78898511
Axis point 98.49093754 127.56704910 0.00000000
Rotation angle (degrees) 159.09569307
Shift along axis -13.52222698
> mmaker #7 to #18
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 copy of 5a0c, chain A (#18) with 5a0c, chain A (#7), sequence
alignment score = 1112.7
RMSD between 218 pruned atom pairs is 0.000 angstroms; (across all 218 pairs:
0.000)
> fitmap #7 inMap #59
Fit molecule 5a0c (#7) to map cryosparc_P371_J1247_003_volume_map (1).mrc
(#59) using 1883 atoms
average map value = 0.0522, steps = 120
shifted from previous position = 3.71
rotated from previous position = 23.2 degrees
atoms outside contour = 1476, contour level = 0.06978
Position of 5a0c (#7) relative to cryosparc_P371_J1247_003_volume_map (1).mrc
(#59) coordinates:
Matrix rotation and translation
-0.93249206 0.31673033 0.17361005 149.49824725
-0.24614085 -0.20547558 -0.94720350 169.75915732
-0.26433545 -0.92599227 0.26956462 154.82905865
Axis 0.02972878 0.61380618 -0.78889681
Axis point 98.47960888 127.58948855 0.00000000
Rotation angle (degrees) 159.09952411
Shift along axis -13.50053159
> volume #61 level 0.07557
> open /Users/amy/Downloads/cryosparc_P483_J188_006_volume_map.mrc
Opened cryosparc_P483_J188_006_volume_map.mrc as #60, grid size 400,400,400,
pixel 0.723, shown at level 0.0122, step 2, values float32
> volume #60 level 0.04049
> hide #7 models
> close #39-56
> transparency #60 50
> show #!57 models
> select add #57
1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 3 models selected
> select subtract #57
Nothing selected
> hide #!57 models
> show #!38 models
> select add #38
6282 atoms, 6138 bonds, 1077 residues, 1 model selected
> view matrix models
> #38,0.70129,-0.71169,-0.041051,59.454,0.277,0.32511,-0.9042,89.328,0.65685,0.62274,0.42514,10.395
> view matrix models
> #38,0.68049,0.72218,0.12406,5.6594,-0.15756,0.30955,-0.93774,159.08,-0.71562,0.61858,0.32443,228.89
> view matrix models
> #38,0.7111,0.6991,0.074864,2.3195,-0.17274,0.27693,-0.94523,162.83,-0.68154,0.65922,0.31769,222.03
> volume flip #60 axis z
Opened cryosparc_P483_J188_006_volume_map.mrc z flip as #39, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> view matrix models
> #38,-0.79214,-0.23105,-0.56492,283.77,0.39756,0.50697,-0.76481,61.539,0.4631,-0.83042,-0.30973,105.99
> view matrix models
> #38,-0.72246,-0.55636,-0.41051,283.31,0.053262,0.54717,-0.83532,115.33,0.68936,-0.62535,-0.36568,63.032
> view matrix models
> #38,-0.72246,-0.55636,-0.41051,283.27,0.053262,0.54717,-0.83532,115.31,0.68936,-0.62535,-0.36568,63.21
> view matrix models
> #38,-0.75346,-0.22412,-0.61812,278.02,0.32917,0.68524,-0.64969,64.051,0.56917,-0.69298,-0.44252,85.775
> view matrix models
> #38,-0.75346,-0.22412,-0.61812,277.72,0.32917,0.68524,-0.64969,62.337,0.56917,-0.69298,-0.44252,89.988
> view matrix models
> #38,-0.75346,-0.22412,-0.61812,274.8,0.32917,0.68524,-0.64969,60.25,0.56917,-0.69298,-0.44252,90.357
> fitmap #38 inMap #39
Fit molecule 9hud (#38) to map cryosparc_P483_J188_006_volume_map.mrc z flip
(#39) using 6282 atoms
average map value = 0.07719, steps = 140
shifted from previous position = 5.69
rotated from previous position = 10.5 degrees
atoms outside contour = 1975, contour level = 0.040487
Position of 9hud (#38) relative to cryosparc_P483_J188_006_volume_map.mrc z
flip (#39) coordinates:
Matrix rotation and translation
-0.69481285 -0.38668893 -0.60638839 274.92375859
0.29518489 0.61552849 -0.73074671 73.34577149
0.65582093 -0.68672881 -0.31353236 73.10268242
Axis 0.03066826 -0.87940971 0.47507687
Axis point 118.71936211 0.00000000 122.64604224
Rotation angle (degrees) 134.13955008
Shift along axis -21.34015667
> mmaker #37 to #38
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 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
score = 1674.4
RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
0.519)
> select subtract #38
Nothing selected
> show #!37 models
> hide #!38 models
> show #!57 models
> mmaker #57 to #37
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 1ezx, chain C (#37) with copy of 1ezx, chain C (#57), sequence
alignment score = 1096
RMSD between 140 pruned atom pairs is 0.000 angstroms; (across all 140 pairs:
0.000)
> hide #!37 models
> select add #57
1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 3 models selected
> view matrix models
> #57,-0.96139,-0.27328,-0.032326,225.27,0.26293,-0.87755,-0.40098,194.89,0.081212,-0.39399,0.91552,76.751
> view matrix models
> #57,-0.98395,-0.080553,-0.1592,229.11,0.11527,-0.96807,-0.2226,199.83,-0.13619,-0.23738,0.96182,88.362
> view matrix models
> #57,-0.98395,-0.080553,-0.1592,229.13,0.11527,-0.96807,-0.2226,200.95,-0.13619,-0.23738,0.96182,87.592
> view matrix models
> #57,-0.94283,-0.24393,0.22707,209.83,0.18457,-0.94952,-0.25367,196.49,0.27748,-0.19726,0.94026,54.255
> view matrix models
> #57,-0.94283,-0.24393,0.22707,211.13,0.18457,-0.94952,-0.25367,198.21,0.27748,-0.19726,0.94026,55.521
> view matrix models
> #57,-0.93042,-0.31273,0.19109,213.56,0.19345,-0.86193,-0.46866,206.45,0.31127,-0.39909,0.86246,61.443
> view matrix models
> #57,-0.93042,-0.31273,0.19109,212.58,0.19345,-0.86193,-0.46866,206.1,0.31127,-0.39909,0.86246,60.836
> view matrix models
> #57,-0.84274,-0.44664,0.3005,202.99,0.29429,-0.84967,-0.43756,196.06,0.45076,-0.28032,0.84749,47.549
> view matrix models
> #57,-0.84274,-0.44664,0.3005,204.01,0.29429,-0.84967,-0.43756,196.43,0.45076,-0.28032,0.84749,48.186
> view matrix models
> #57,-0.84274,-0.44664,0.3005,205.89,0.29429,-0.84967,-0.43756,195.12,0.45076,-0.28032,0.84749,50.177
> view matrix models
> #57,-0.40829,-0.80923,0.42242,172.87,0.75449,-0.55964,-0.34285,146.27,0.51385,0.17873,0.83905,34.853
> view matrix models
> #57,-0.40829,-0.80923,0.42242,177.69,0.75449,-0.55964,-0.34285,148.99,0.51385,0.17873,0.83905,33.682
> view matrix models
> #57,-0.26229,-0.78164,0.56591,157.89,0.82741,-0.48394,-0.28493,138.37,0.49658,0.39351,0.77367,33.446
> view matrix models
> #57,-0.50448,-0.84508,0.17704,198.87,0.77252,-0.53335,-0.34461,147.01,0.38565,-0.037082,0.9219,44.834
> view matrix models
> #57,-0.50448,-0.84508,0.17704,197.7,0.77252,-0.53335,-0.34461,146.01,0.38565,-0.037082,0.9219,43.5
> view matrix models
> #57,-0.55352,-0.81516,0.17067,201.3,0.76006,-0.57821,-0.29661,145.6,0.34047,-0.03446,0.93962,46.193
> view matrix models
> #57,-0.55352,-0.81516,0.17067,201,0.76006,-0.57821,-0.29661,144.01,0.34047,-0.03446,0.93962,46.083
> view matrix models
> #57,0.19927,-0.70806,0.67745,111.26,0.40682,-0.56916,-0.71453,193.98,0.89151,0.41799,0.17463,30.057
> fitmap #57 inMap #39
Fit molecule copy of 1ezx (#57) to map cryosparc_P483_J188_006_volume_map.mrc
z flip (#39) using 1009 atoms
average map value = 0.0293, steps = 168
shifted from previous position = 3.46
rotated from previous position = 14.9 degrees
atoms outside contour = 704, contour level = 0.040487
Position of copy of 1ezx (#57) relative to
cryosparc_P483_J188_006_volume_map.mrc z flip (#39) coordinates:
Matrix rotation and translation
-0.00776067 -0.76663470 0.64203663 129.30975418
0.53267917 -0.54654599 -0.64617367 178.30805215
0.84628169 0.33698479 0.41261190 20.94708234
Axis 0.59871569 -0.12437946 0.79124539
Axis point -5.11418337 119.30863791 0.00000000
Rotation angle (degrees) 124.80933717
Shift along axis 71.81620095
> view matrix models
> #57,-0.84354,-0.47018,0.25957,209.7,0.35522,-0.85092,-0.38698,186.48,0.40282,-0.23422,0.8848,45.964
> view matrix models
> #57,-0.84354,-0.47018,0.25957,210.5,0.35522,-0.85092,-0.38698,187.68,0.40282,-0.23422,0.8848,46.627
> view matrix models
> #57,-0.91572,-0.40165,-0.011594,228.63,0.39352,-0.89061,-0.22795,177.36,0.081229,-0.2133,0.9736,67.651
> view matrix models
> #57,-0.91572,-0.40165,-0.011594,228.49,0.39352,-0.89061,-0.22795,177.31,0.081229,-0.2133,0.9736,67.495
> fitmap #57 inMap #39
Fit molecule copy of 1ezx (#57) to map cryosparc_P483_J188_006_volume_map.mrc
z flip (#39) using 1009 atoms
average map value = 0.03023, steps = 128
shifted from previous position = 2.17
rotated from previous position = 27.6 degrees
atoms outside contour = 692, contour level = 0.040487
Position of copy of 1ezx (#57) relative to
cryosparc_P483_J188_006_volume_map.mrc z flip (#39) coordinates:
Matrix rotation and translation
-0.97588300 -0.21795429 0.01217931 226.13416383
0.16332980 -0.76604383 -0.62169145 212.61271533
0.14483021 -0.60470887 0.78316756 80.91608083
Axis 0.04203015 -0.32829732 0.94363888
Axis point 99.48152797 132.57508735 0.00000000
Rotation angle (degrees) 168.34438880
Shift along axis 16.05982811
> select subtract #57
Nothing selected
> volume gaussian #39 sDev 2
Opened cryosparc_P483_J188_006_volume_map.mrc z flip gaussian as #40, grid
size 400,400,400, pixel 0.723, shown at step 1, values float32
> open /Users/amy/Downloads/cryosparc_P483_molmap_of_combined_6A.mrc
Opened cryosparc_P483_molmap_of_combined_6A.mrc as #41, grid size 200,200,200,
pixel 1, shown at level 0.293, step 1, values float32
> transparency #41 50
> show #!37 models
> select add #37
3984 atoms, 3982 bonds, 5 pseudobonds, 592 residues, 3 models selected
> view matrix models
> #37,-0.96139,-0.27328,-0.032326,218.59,0.26293,-0.87755,-0.40098,146.69,0.081212,-0.39399,0.91552,81.851
> view matrix models
> #37,-0.049922,0.49391,-0.86808,164.61,0.32699,-0.81318,-0.48148,143.6,-0.94371,-0.30789,-0.12091,207.3
> view matrix models
> #37,0.78493,0.53816,-0.30703,72.795,0.33958,-0.78815,-0.51332,143.29,-0.51824,0.29866,-0.80139,186.1
> view matrix models
> #37,0.48345,-0.22115,0.84698,66.159,0.004741,-0.96689,-0.25517,160.69,0.87536,0.12738,-0.46639,79.548
> view matrix models
> #37,-0.49427,-0.19074,0.84812,131.98,0.13352,-0.98071,-0.14275,146.1,0.85899,0.04269,0.51021,29.25
> view matrix models
> #37,-0.87073,-0.2065,0.44631,181.66,0.14198,-0.97448,-0.17389,146.97,0.47082,-0.088043,0.87782,41.66
> view matrix models
> #37,-0.87073,-0.2065,0.44631,183.6,0.14198,-0.97448,-0.17389,140.36,0.47082,-0.088043,0.87782,41.006
> view matrix models
> #37,-0.83015,0.067283,-0.55346,223.99,0.083286,-0.96659,-0.24243,147.91,-0.55128,-0.24735,0.79681,124.17
> view matrix models
> #37,-0.83015,0.067283,-0.55346,229.16,0.083286,-0.96659,-0.24243,155.6,-0.55128,-0.24735,0.79681,121.21
> view matrix models
> #37,-0.76415,-0.19095,-0.61612,241.25,0.333,-0.93483,-0.12329,129.98,-0.55243,-0.29938,0.77794,124.99
> fitmap #37 inMap #41
Fit molecule 1ezx (#37) to map cryosparc_P483_molmap_of_combined_6A.mrc (#41)
using 3984 atoms
average map value = 0.4227, steps = 272
shifted from previous position = 34.2
rotated from previous position = 34.8 degrees
atoms outside contour = 366, contour level = 0.29336
Position of 1ezx (#37) relative to cryosparc_P483_molmap_of_combined_6A.mrc
(#41) coordinates:
Matrix rotation and translation
-0.39076986 0.10890222 -0.91402362 198.79794072
0.07022585 -0.98655567 -0.14756757 150.28581374
-0.91780564 -0.12185304 0.37786848 136.15090391
Axis 0.55183393 0.08116225 -0.82999519
Axis point 145.70964793 80.43889324 0.00000000
Rotation angle (degrees) 178.66493597
Shift along axis 8.89638759
> mmaker #7 to #37
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 1ezx, chain C (#37) with 5a0c, chain A (#7), sequence alignment
score = 241.2
RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
3.073)
> show #7 models
> show #!8 models
> mmaker #8 to #7
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 5a0c, chain A (#7) with 1ezx, chain C (#8), sequence alignment
score = 241.2
RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
3.073)
> select #8/A
2686 atoms, 2674 bonds, 398 residues, 1 model selected
> delete #8/A
> select #8/B
289 atoms, 294 bonds, 39 residues, 1 model selected
> delete #8/B
> close #8
> show #!31 models
> mmaker #31 t o#7
> matchmaker #31 to o#7
Invalid "to" argument: invalid atoms specifier
> mmaker #31 t to#7
> matchmaker #31 to to#7
Invalid "to" argument: invalid atoms specifier
> mmaker #31 to #7
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 5a0c, chain A (#7) with copy of copy of copy of 1ezx, chain A
(#31), sequence alignment score = 25.4
RMSD between 4 pruned atom pairs is 1.006 angstroms; (across all 34 pairs:
19.211)
> mmaker #31 to #37
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 1ezx, chain A (#37) with copy of copy of copy of 1ezx, chain A
(#31), sequence alignment score = 1734
RMSD between 335 pruned atom pairs is 0.000 angstroms; (across all 335 pairs:
0.000)
> hide #!37 models
> hide #!41 models
> hide #!57 models
> combine #7,31 modelId #42 name AATHNEcombined
Remapping chain ID 'A' in copy of copy of copy of 1ezx #31 to 'C'
> hide #!31 models
> hide #7 models
> molmap #42 6
Opened AATHNEcombined map 6 as #8, grid size 43,51,63, pixel 2, shown at level
0.107, step 1, values float32
> volume #8 level 0.4678
> hide #!42 models
> volume #8 level 0.4143
> transparency #8 50
> show #!29 models
> select add #8
2 models selected
> view matrix models
> #8,-0.94731,0.3033,-0.10305,152.68,-0.052376,-0.46403,-0.88427,177.46,-0.31602,-0.83228,0.45547,210.1
> view matrix models
> #8,-0.67966,0.68715,-0.25667,146.07,0.0014291,-0.34867,-0.93725,176.15,-0.73352,-0.63738,0.23599,220.93
> select subtract #8
Nothing selected
> select add #8
2 models selected
> view matrix models
> #8,-0.80209,0.59535,-0.046957,144.36,-0.15685,-0.28587,-0.94534,180.87,-0.57624,-0.75089,0.32268,217.17
> view matrix models
> #8,-0.98552,0.057058,-0.15966,159.48,0.11645,-0.45668,-0.88198,176.33,-0.12324,-0.8878,0.44342,206.47
> select subtract #8
Nothing selected
> fitmap #8 inMap #29
Fit map AATHNEcombined map 6 in map J1122.mrc using 3370 points
correlation = -0.06744, correlation about mean = 0.03351, overlap = -0.3948
steps = 72, shift = 3.07, angle = 5.37 degrees
Position of AATHNEcombined map 6 (#8) relative to J1122.mrc (#29) coordinates:
Matrix rotation and translation
-0.99402372 -0.01790342 -0.10768616 160.40909895
0.10457674 -0.43913839 -0.89231227 175.73306960
-0.03131369 -0.89824103 0.43838626 207.83747749
Axis -0.04104025 -0.52866794 0.84783601
Axis point 80.62201678 156.15315639 0.00000000
Rotation angle (degrees) 175.85785915
Shift along axis 76.72442836
> volume #8 level 0.3659
> view
> volume #29 level 0.06441
> show #!42 models
> select add #42
4858 atoms, 4713 bonds, 831 residues, 1 model selected
> view matrix models
> #42,-0.94731,0.3033,-0.10305,202.51,-0.052376,-0.46403,-0.88427,151.25,-0.31602,-0.83228,0.45547,188.42
> view matrix models
> #42,-0.065313,0.66691,-0.74227,198.13,-0.22175,-0.73496,-0.64083,151.68,-0.97291,0.12274,0.19589,194.19
> view matrix models
> #42,0.76996,0.12763,-0.6252,186.82,-0.51684,-0.44988,-0.72835,155.58,-0.37422,0.88392,-0.28042,184.85
> view matrix models
> #42,0.26956,0.68406,-0.67779,189.68,-0.23721,-0.63498,-0.73521,153.14,-0.93331,0.35896,-0.0088999,195.67
> view matrix models
> #42,0.16808,0.4812,-0.86035,199.68,0.12383,-0.87616,-0.46585,142.27,-0.97797,-0.028238,-0.20685,207.72
> view matrix models
> #42,0.16808,0.4812,-0.86035,176.9,0.12383,-0.87616,-0.46585,168.91,-0.97797,-0.028238,-0.20685,243.77
> view matrix models
> #42,-0.098371,0.74921,-0.65499,172.34,0.16185,-0.63737,-0.75337,172.69,-0.9819,-0.18012,-0.058563,241.94
> view matrix models
> #42,-0.098371,0.74921,-0.65499,168.3,0.16185,-0.63737,-0.75337,164.55,-0.9819,-0.18012,-0.058563,240.14
> fitmap #42 inMap #8
Fit molecule AATHNEcombined (#42) to map AATHNEcombined map 6 (#8) using 4858
atoms
average map value = 0.4401, steps = 236
shifted from previous position = 23.5
rotated from previous position = 81.6 degrees
atoms outside contour = 1171, contour level = 0.36586
Position of AATHNEcombined (#42) relative to AATHNEcombined map 6 (#8)
coordinates:
Matrix rotation and translation
0.99999997 0.00012320 0.00021381 -0.02142066
-0.00012322 0.99999999 0.00009509 0.00213481
-0.00021379 -0.00009512 0.99999997 0.00632785
Axis -0.35962131 0.80845713 -0.46590727
Axis point 43.71009619 0.00000000 89.29249519
Rotation angle (degrees) 0.01515213
Shift along axis 0.00648103
> select subtract #42
Nothing selected
> hide #!42 models
> show #!42 models
> combine #42 close false
> select add #43
4858 atoms, 4713 bonds, 831 residues, 1 model selected
> view matrix models
> #43,-0.994,-0.018016,-0.1079,166.09,0.10482,-0.43904,-0.89233,181.76,-0.031297,-0.89829,0.43829,253.22
> view matrix models
> #43,-0.994,-0.018016,-0.1079,167.72,0.10482,-0.43904,-0.89233,183.32,-0.031297,-0.89829,0.43829,266.56
> select subtract #43
Nothing selected
> hide #!42 models
> select add #43/A:94
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #43/A:93
20 atoms, 19 bonds, 2 residues, 1 model selected
> select add #43/A:92
28 atoms, 26 bonds, 3 residues, 1 model selected
> select add #43/A:91
39 atoms, 36 bonds, 4 residues, 1 model selected
> select add #43/A:90
48 atoms, 44 bonds, 5 residues, 1 model selected
> select add #43/A:89
55 atoms, 50 bonds, 6 residues, 1 model selected
> select add #43/A:88
60 atoms, 54 bonds, 7 residues, 1 model selected
> select add #43/A:87
71 atoms, 65 bonds, 8 residues, 1 model selected
> select add #43/A:86
78 atoms, 71 bonds, 9 residues, 1 model selected
> select subtract #43/A:86
71 atoms, 65 bonds, 8 residues, 1 model selected
> select add #43/A:86
78 atoms, 71 bonds, 9 residues, 1 model selected
> select add #43/A:85
87 atoms, 79 bonds, 10 residues, 1 model selected
> select add #43/A:84
98 atoms, 89 bonds, 11 residues, 1 model selected
> select add #43/A:83
105 atoms, 95 bonds, 12 residues, 1 model selected
> select add #43/A:82
112 atoms, 102 bonds, 13 residues, 1 model selected
> select add #43/A:81
121 atoms, 110 bonds, 14 residues, 1 model selected
> select add #43/A:80
132 atoms, 120 bonds, 15 residues, 1 model selected
> select add #43/A:79
143 atoms, 130 bonds, 16 residues, 1 model selected
> select add #43/A:77
151 atoms, 137 bonds, 17 residues, 1 model selected
> select add #43/A:78
157 atoms, 142 bonds, 18 residues, 1 model selected
> select add #43/A:76
165 atoms, 149 bonds, 19 residues, 1 model selected
> select add #43/A:75
175 atoms, 159 bonds, 20 residues, 1 model selected
> select add #43/A:74
180 atoms, 163 bonds, 21 residues, 1 model selected
> select add #43/A:73
184 atoms, 166 bonds, 22 residues, 1 model selected
> select add #43/A:72
192 atoms, 173 bonds, 23 residues, 1 model selected
> select add #43/A:71
199 atoms, 179 bonds, 24 residues, 1 model selected
> select add #43/A:70
206 atoms, 185 bonds, 25 residues, 1 model selected
> select add #43/A:69
217 atoms, 195 bonds, 26 residues, 1 model selected
> select add #43/A:54
223 atoms, 200 bonds, 27 residues, 1 model selected
> select subtract #43/A:54
217 atoms, 195 bonds, 26 residues, 1 model selected
> select add #43/A:68
224 atoms, 201 bonds, 27 residues, 1 model selected
> select add #43/A:66
229 atoms, 205 bonds, 28 residues, 1 model selected
> select add #43/A:65
240 atoms, 215 bonds, 29 residues, 1 model selected
> select add #43/A:64
247 atoms, 221 bonds, 30 residues, 1 model selected
> select add #43/A:63
255 atoms, 228 bonds, 31 residues, 1 model selected
> select add #43/A:62
262 atoms, 234 bonds, 32 residues, 1 model selected
> select add #43/A:61
270 atoms, 241 bonds, 33 residues, 1 model selected
> select add #43/A:60
275 atoms, 245 bonds, 34 residues, 1 model selected
> select add #43/A:59
282 atoms, 251 bonds, 35 residues, 1 model selected
> select add #43/A:58
288 atoms, 256 bonds, 36 residues, 1 model selected
> select add #43/A:57
298 atoms, 266 bonds, 37 residues, 1 model selected
> select add #43/A:56
303 atoms, 270 bonds, 38 residues, 1 model selected
> select add #43/A:55
308 atoms, 274 bonds, 39 residues, 1 model selected
> select add #43/A:54
314 atoms, 279 bonds, 40 residues, 1 model selected
> select add #43/A:53
322 atoms, 286 bonds, 41 residues, 1 model selected
> select add #43/A:52
329 atoms, 292 bonds, 42 residues, 1 model selected
> select add #43/A:51
340 atoms, 303 bonds, 43 residues, 1 model selected
> select add #43/A:50
348 atoms, 310 bonds, 44 residues, 1 model selected
> select add #43/A:48
353 atoms, 314 bonds, 45 residues, 1 model selected
> select add #43/A:47
361 atoms, 321 bonds, 46 residues, 1 model selected
> select add #43/A:46
369 atoms, 328 bonds, 47 residues, 1 model selected
> select subtract #43/A:46
361 atoms, 321 bonds, 46 residues, 1 model selected
> select add #43/A:45
368 atoms, 327 bonds, 47 residues, 1 model selected
> select add #43/A:46
376 atoms, 334 bonds, 48 residues, 1 model selected
> select add #43/A:44
381 atoms, 338 bonds, 49 residues, 1 model selected
> select add #43/A:43
385 atoms, 341 bonds, 50 residues, 1 model selected
> select add #43/A:42
391 atoms, 346 bonds, 51 residues, 1 model selected
> select add #43/A:41
402 atoms, 357 bonds, 52 residues, 1 model selected
> select add #43/A:40
412 atoms, 367 bonds, 53 residues, 1 model selected
> select add #43/A:39
416 atoms, 370 bonds, 54 residues, 1 model selected
> color sel forest green
> select clear
> select add #43/A:49
7 atoms, 7 bonds, 1 residue, 1 model selected
> color sel forest green
> select clear
> select add #43/A:38
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #43/A:36
15 atoms, 13 bonds, 2 residues, 1 model selected
> select add #43/A:35
23 atoms, 20 bonds, 3 residues, 1 model selected
> select add #43/A:34
32 atoms, 28 bonds, 4 residues, 1 model selected
> select add #43/A:33
40 atoms, 35 bonds, 5 residues, 1 model selected
> select add #43/A:32
46 atoms, 40 bonds, 6 residues, 1 model selected
> select subtract #43/A:32
40 atoms, 35 bonds, 5 residues, 1 model selected
> select add #43/A:32
46 atoms, 40 bonds, 6 residues, 1 model selected
> select add #43/A:31
53 atoms, 46 bonds, 7 residues, 1 model selected
> select add #43/A:30
61 atoms, 53 bonds, 8 residues, 1 model selected
> color sel forest green
> select clear
> select add #43/A:108
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #43/A:109
15 atoms, 13 bonds, 2 residues, 1 model selected
> select add #43/A:110
23 atoms, 20 bonds, 3 residues, 1 model selected
> select add #43/A:111
32 atoms, 28 bonds, 4 residues, 1 model selected
> select add #43/A:112
40 atoms, 35 bonds, 5 residues, 1 model selected
> color sel cyan
> select add #43/A:90
49 atoms, 43 bonds, 6 residues, 1 model selected
> select add #43/A:91
60 atoms, 53 bonds, 7 residues, 1 model selected
> select add #43/A:92
68 atoms, 60 bonds, 8 residues, 1 model selected
> select add #43/A:93
79 atoms, 71 bonds, 9 residues, 1 model selected
> select add #43/A:94
88 atoms, 79 bonds, 10 residues, 1 model selected
> color sel cyan
> select add #43/A:54
94 atoms, 84 bonds, 11 residues, 1 model selected
> select add #43/A:53
102 atoms, 91 bonds, 12 residues, 1 model selected
> select add #43/A:52
109 atoms, 97 bonds, 13 residues, 1 model selected
> select add #43/A:51
120 atoms, 108 bonds, 14 residues, 1 model selected
> color sel cyan
> select clear
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> hide #!43 models
> show #!43 models
> combine #43 close false
> select add #44
4858 atoms, 4713 bonds, 831 residues, 1 model selected
> view matrix models
> #44,-0.994,-0.018016,-0.1079,181.57,0.10482,-0.43904,-0.89233,189.57,-0.031297,-0.89829,0.43829,312.85
> select subtract #44
Nothing selected
> select add #44/A:127
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #44/A:128
15 atoms, 14 bonds, 2 residues, 1 model selected
> delete sel
> select add #44/A:129
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #44/A:130
14 atoms, 12 bonds, 2 residues, 1 model selected
> select add #44/A:131
18 atoms, 15 bonds, 3 residues, 1 model selected
> select add #44/A:132
29 atoms, 25 bonds, 4 residues, 1 model selected
> select add #44/A:133
40 atoms, 35 bonds, 5 residues, 1 model selected
> select add #44/A:134
48 atoms, 42 bonds, 6 residues, 1 model selected
> select subtract #44/A:134
40 atoms, 35 bonds, 5 residues, 1 model selected
> select add #44/A:134
48 atoms, 42 bonds, 6 residues, 1 model selected
> select add #44/A:135
52 atoms, 45 bonds, 7 residues, 1 model selected
> select add #44/A:136
60 atoms, 52 bonds, 8 residues, 1 model selected
> select add #44/A:137
64 atoms, 55 bonds, 9 residues, 1 model selected
> select add #44/A:138
71 atoms, 61 bonds, 10 residues, 1 model selected
> delete sel
> select add #44/A:96
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #44/A:97
12 atoms, 10 bonds, 2 residues, 1 model selected
> select add #44/A:98
24 atoms, 22 bonds, 3 residues, 1 model selected
> select add #44/A:99
32 atoms, 29 bonds, 4 residues, 1 model selected
> select add #44/A:100
39 atoms, 36 bonds, 5 residues, 1 model selected
> select add #44/A:101
46 atoms, 42 bonds, 6 residues, 1 model selected
> select add #44/A:102
54 atoms, 49 bonds, 7 residues, 1 model selected
> select add #44/A:103
62 atoms, 56 bonds, 8 residues, 1 model selected
> select add #44/A:104
70 atoms, 63 bonds, 9 residues, 1 model selected
> select add #44/A:105
78 atoms, 70 bonds, 10 residues, 1 model selected
> select add #44/A:106
86 atoms, 77 bonds, 11 residues, 1 model selected
> select add #44/A:107
94 atoms, 84 bonds, 12 residues, 1 model selected
> delete sel
> select clear
> select add #44/A:160
9 atoms, 8 bonds, 1 residue, 1 model selected
> select subtract #44/A:160
Nothing selected
> select #44/A:159
8 atoms, 7 bonds, 1 residue, 1 model selected
> select subtract #44/A:159
Nothing selected
> select add #44/A:159
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #44/A:158
15 atoms, 13 bonds, 2 residues, 1 model selected
> select add #44/A:157
21 atoms, 18 bonds, 3 residues, 1 model selected
> select add #44/A:156
26 atoms, 22 bonds, 4 residues, 1 model selected
> select add #44/A:155
34 atoms, 29 bonds, 5 residues, 1 model selected
> select add #44/A:154
38 atoms, 32 bonds, 6 residues, 1 model selected
> select add #44/A:152
49 atoms, 42 bonds, 7 residues, 1 model selected
> select add #44/A:151
57 atoms, 49 bonds, 8 residues, 1 model selected
> select add #44/A:150
68 atoms, 59 bonds, 9 residues, 1 model selected
> select add #44/A:149
72 atoms, 62 bonds, 10 residues, 1 model selected
> select add #44/A:148
80 atoms, 69 bonds, 11 residues, 1 model selected
> select add #44/A:147
88 atoms, 76 bonds, 12 residues, 1 model selected
> select add #44/A:146
92 atoms, 79 bonds, 13 residues, 1 model selected
> select add #44/A:145
106 atoms, 94 bonds, 14 residues, 1 model selected
> delete sel
> select add #44/A:113
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #44/A:114
12 atoms, 10 bonds, 2 residues, 1 model selected
> select add #44/A:115
18 atoms, 15 bonds, 3 residues, 1 model selected
> select add #44/A:116
23 atoms, 19 bonds, 4 residues, 1 model selected
> select add #44/A:117
30 atoms, 25 bonds, 5 residues, 1 model selected
> select add #44/A:118
38 atoms, 32 bonds, 6 residues, 1 model selected
> select add #44/A:119
46 atoms, 39 bonds, 7 residues, 1 model selected
> select add #44/A:120
51 atoms, 43 bonds, 8 residues, 1 model selected
> select add #44/A:121
59 atoms, 50 bonds, 9 residues, 1 model selected
> select add #44/A:122
66 atoms, 56 bonds, 10 residues, 1 model selected
> select add #44/A:124
73 atoms, 62 bonds, 11 residues, 1 model selected
> select add #44/A:125
78 atoms, 66 bonds, 12 residues, 1 model selected
> select add #44/A:126
87 atoms, 74 bonds, 13 residues, 1 model selected
> delete sel
> open /Users/amy/Downloads/emd_8220.map
Opened emd_8220.map as #45, grid size 100,86,100, pixel 0.554,0.564,0.577,
shown at level 0.0696, step 1, values float32
> volume #45 level 0.05639
> close #45
> select add #44/A:16
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #44/A:17
15 atoms, 13 bonds, 2 residues, 1 model selected
> select add #44/A:18
19 atoms, 16 bonds, 3 residues, 1 model selected
> select add #44/A:19
23 atoms, 19 bonds, 4 residues, 1 model selected
> select add #44/A:20
34 atoms, 29 bonds, 5 residues, 1 model selected
> select add #44/A:21
45 atoms, 39 bonds, 6 residues, 1 model selected
> select add #44/A:22
50 atoms, 43 bonds, 7 residues, 1 model selected
> select add #44/A:23
61 atoms, 53 bonds, 8 residues, 1 model selected
> select add #44/A:24
68 atoms, 60 bonds, 9 residues, 1 model selected
> select add #44/A:25
78 atoms, 70 bonds, 10 residues, 1 model selected
> select add #44/A:26
83 atoms, 74 bonds, 11 residues, 1 model selected
> select add #44/A:27
97 atoms, 89 bonds, 12 residues, 1 model selected
> select add #44/A:29
108 atoms, 100 bonds, 13 residues, 1 model selected
> delete sel
> select add #44
4377 atoms, 4217 bonds, 5 pseudobonds, 767 residues, 2 models selected
> view matrix models
> #44,-0.994,-0.018016,-0.1079,167.02,0.10482,-0.43904,-0.89233,176.04,-0.031297,-0.89829,0.43829,207.55
> fitmap #44 inMap #8
Fit molecule copy of copy of AATHNEcombined (#44) to map AATHNEcombined map 6
(#8) using 4377 atoms
average map value = 0.4393, steps = 56
shifted from previous position = 6.58
rotated from previous position = 0.0611 degrees
atoms outside contour = 1072, contour level = 0.36586
Position of copy of copy of AATHNEcombined (#44) relative to AATHNEcombined
map 6 (#8) coordinates:
Matrix rotation and translation
0.99999971 0.00068256 0.00033276 -0.05114740
-0.00068229 0.99999944 -0.00080618 0.06249724
-0.00033331 0.00080595 0.99999962 -0.02902612
Axis 0.72788203 0.30072989 -0.61623801
Axis point 0.00000000 36.47000800 77.70180160
Rotation angle (degrees) 0.06345003
Shift along axis -0.00054749
> view matrix models
> #44,-0.99398,-0.018669,-0.108,161.2,0.10517,-0.43979,-0.89192,171.06,-0.030847,-0.89791,0.4391,163.49
> view matrix models
> #44,-0.99398,-0.018669,-0.108,160.92,0.10517,-0.43979,-0.89192,163.66,-0.030847,-0.89791,0.4391,148.99
> fitmap #44 inMap #29
Fit molecule copy of copy of AATHNEcombined (#44) to map J1122.mrc (#29) using
4377 atoms
average map value = 0.08017, steps = 120
shifted from previous position = 10.4
rotated from previous position = 19 degrees
atoms outside contour = 1934, contour level = 0.064406
Position of copy of copy of AATHNEcombined (#44) relative to J1122.mrc (#29)
coordinates:
Matrix rotation and translation
-0.93560766 0.29367131 -0.19594762 148.33622912
0.04403975 -0.45360760 -0.89011271 165.90577632
-0.35028390 -0.84142576 0.41146553 152.50362608
Axis 0.16365385 0.51877807 -0.83909876
Axis point 96.84111132 123.35674227 0.00000000
Rotation angle (degrees) 171.44551676
Shift along axis -17.62152966
> view matrix models
> #44,-0.93561,0.29367,-0.19595,147.21,0.04404,-0.45361,-0.89011,177.11,-0.35028,-0.84143,0.41147,212.36
> view matrix models
> #44,-0.93561,0.29367,-0.19595,156.61,0.04404,-0.45361,-0.89011,178.01,-0.35028,-0.84143,0.41147,216.59
> fitmap #44 inMap #8
Fit molecule copy of copy of AATHNEcombined (#44) to map AATHNEcombined map 6
(#8) using 4377 atoms
average map value = 0.4394, steps = 64
shifted from previous position = 3.67
rotated from previous position = 19 degrees
atoms outside contour = 1073, contour level = 0.36586
Position of copy of copy of AATHNEcombined (#44) relative to AATHNEcombined
map 6 (#8) coordinates:
Matrix rotation and translation
0.99999986 0.00044110 -0.00029615 0.00647815
-0.00044140 0.99999940 -0.00099710 0.04994382
0.00029571 0.00099723 0.99999946 -0.05779749
Axis 0.88254618 -0.26191484 -0.39052893
Axis point 0.00000000 52.03151904 54.05257298
Rotation angle (degrees) 0.06473724
Shift along axis 0.01520783
> view matrix models
> #44,-0.99405,-0.018449,-0.10737,168.43,0.10451,-0.43998,-0.8919,162.5,-0.030788,-0.89782,0.43929,154.17
> view matrix models
> #44,-0.99405,-0.018449,-0.10737,153.97,0.10451,-0.43998,-0.8919,165.28,-0.030788,-0.89782,0.43929,147.12
> fitmap #44 inMap #29
Fit molecule copy of copy of AATHNEcombined (#44) to map J1122.mrc (#29) using
4377 atoms
average map value = 0.08017, steps = 112
shifted from previous position = 3.23
rotated from previous position = 19 degrees
atoms outside contour = 1936, contour level = 0.064406
Position of copy of copy of AATHNEcombined (#44) relative to J1122.mrc (#29)
coordinates:
Matrix rotation and translation
-0.93553950 0.29370365 -0.19622436 148.34392039
0.04417583 -0.45387692 -0.88996867 165.89259865
-0.35044876 -0.84126922 0.41164519 152.49532201
Axis 0.16377458 0.51865136 -0.83915354
Axis point 96.84939042 123.33620103 0.00000000
Rotation angle (degrees) 171.44966078
Shift along axis -17.63160462
> select add #8
4377 atoms, 4217 bonds, 5 pseudobonds, 767 residues, 4 models selected
> select subtract #44
2 models selected
> view matrix models
> #8,-0.94817,0.24716,-0.1997,158.38,0.060761,-0.47584,-0.87743,176.64,-0.31189,-0.84409,0.43616,212.3
> select subtract #8
Nothing selected
> select add #44
4377 atoms, 4217 bonds, 5 pseudobonds, 767 residues, 2 models selected
> view matrix models
> #44,-0.93554,0.2937,-0.19622,141.41,0.044176,-0.45388,-0.88997,179.93,-0.35045,-0.84127,0.41165,213.18
> view matrix models
> #44,-0.93554,0.2937,-0.19622,151.53,0.044176,-0.45388,-0.88997,179.57,-0.35045,-0.84127,0.41165,212.38
> view matrix models
> #44,-0.93554,0.2937,-0.19622,155.41,0.044176,-0.45388,-0.88997,178.43,-0.35045,-0.84127,0.41165,216.37
> view matrix models
> #44,-0.93554,0.2937,-0.19622,155.54,0.044176,-0.45388,-0.88997,176.75,-0.35045,-0.84127,0.41165,213.56
> view matrix models
> #44,-0.93554,0.2937,-0.19622,156.39,0.044176,-0.45388,-0.88997,176.3,-0.35045,-0.84127,0.41165,214.67
> fitmap #44 inMap #8
Fit molecule copy of copy of AATHNEcombined (#44) to map AATHNEcombined map 6
(#8) using 4377 atoms
average map value = 0.4394, steps = 52
shifted from previous position = 1.68
rotated from previous position = 3.02 degrees
atoms outside contour = 1076, contour level = 0.36586
Position of copy of copy of AATHNEcombined (#44) relative to AATHNEcombined
map 6 (#8) coordinates:
Matrix rotation and translation
0.99999955 0.00082150 0.00046001 -0.00883030
-0.00082119 0.99999944 -0.00066348 0.04456765
-0.00046055 0.00066310 0.99999967 -0.03206776
Axis 0.57592008 0.39965178 -0.71315813
Axis point 36.92441346 35.72354775 0.00000000
Rotation angle (degrees) 0.06598750
Shift along axis 0.03559538
> select subtract #44
Nothing selected
> hide #!44 models
> select add #43
4858 atoms, 4713 bonds, 831 residues, 1 model selected
> select subtract #43
Nothing selected
> show #!44 models
> select add #44
4377 atoms, 4217 bonds, 5 pseudobonds, 767 residues, 2 models selected
> view matrix models
> #44,-0.94828,0.24625,-0.2003,158.56,0.061556,-0.47637,-0.87709,164.14,-0.3114,-0.84406,0.43658,152.21
> view matrix models
> #44,-0.94828,0.24625,-0.2003,153.59,0.061556,-0.47637,-0.87709,162.81,-0.3114,-0.84406,0.43658,148.12
> fitmap #44 inMap #29
Fit molecule copy of copy of AATHNEcombined (#44) to map J1122.mrc (#29) using
4377 atoms
average map value = 0.08017, steps = 96
shifted from previous position = 5.9
rotated from previous position = 3.02 degrees
atoms outside contour = 1937, contour level = 0.064406
Position of copy of copy of AATHNEcombined (#44) relative to J1122.mrc (#29)
coordinates:
Matrix rotation and translation
-0.93556337 0.29370123 -0.19611414 148.34082953
0.04407128 -0.45387887 -0.88997286 165.89641444
-0.35039819 -0.84126901 0.41168865 152.49037322
Axis 0.16372475 0.51864729 -0.83916578
Axis point 96.84588182 123.33307757 0.00000000
Rotation angle (degrees) 171.44626082
Shift along axis -17.63591277
> view matrix models
> #44,-0.93556,0.2937,-0.19611,181.55,0.044071,-0.45388,-0.88997,200.58,-0.3504,-0.84127,0.41169,325.24
> volume #29 level 0.05579
> volume #29 level 0.0639
> select subtract #44
Nothing selected
> select add #44/A:83
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #44/A:81
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #44/A:82
23 atoms, 21 bonds, 3 residues, 1 model selected
> select add #44/A:80
34 atoms, 31 bonds, 4 residues, 1 model selected
> select add #44/A:79
45 atoms, 41 bonds, 5 residues, 1 model selected
> select add #44/A:78
51 atoms, 46 bonds, 6 residues, 1 model selected
> select add #44/A:77
59 atoms, 53 bonds, 7 residues, 1 model selected
> select add #44/A:76
67 atoms, 60 bonds, 8 residues, 1 model selected
> select add #44/A:75
77 atoms, 70 bonds, 9 residues, 1 model selected
> delete sel
> select add #44/A:231
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #44/A:230
10 atoms, 8 bonds, 2 residues, 1 model selected
> select add #44/A:228
15 atoms, 12 bonds, 3 residues, 1 model selected
> select add #44/A:227
21 atoms, 17 bonds, 4 residues, 1 model selected
> select add #44/A:226
25 atoms, 20 bonds, 5 residues, 1 model selected
> select add #44/A:232
33 atoms, 27 bonds, 6 residues, 1 model selected
> select add #44/A:143
41 atoms, 34 bonds, 7 residues, 1 model selected
> select subtract #44/A:143
33 atoms, 27 bonds, 6 residues, 1 model selected
> select add #44/A:233
45 atoms, 39 bonds, 7 residues, 1 model selected
> delete sel
> select add #44/A:190
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #44/A:191
15 atoms, 13 bonds, 2 residues, 1 model selected
> select add #44/A:192
26 atoms, 23 bonds, 3 residues, 1 model selected
> select add #44/A:194
35 atoms, 31 bonds, 4 residues, 1 model selected
> select add #44/A:195
40 atoms, 35 bonds, 5 residues, 1 model selected
> select add #44/A:196
44 atoms, 38 bonds, 6 residues, 1 model selected
> delete sel
> select add #44/A:197
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #44/A:198
13 atoms, 11 bonds, 2 residues, 1 model selected
> delete sel
> hide #!44 models
> show #!44 models
> molmap #44 6
Opened copy of copy of AATHNEcombined map 6 as #45, grid size 43,51,63, pixel
2, shown at level 0.0888, step 1, values float32
> close #45
> molmap #44 4
Opened copy of copy of AATHNEcombined map 4 as #45, grid size 55,68,86, pixel
1.33, shown at level 0.0965, step 1, values float32
> hide #!45 models
> close #45
> molmap #44 6
Opened copy of copy of AATHNEcombined map 6 as #45, grid size 43,51,63, pixel
2, shown at level 0.0888, step 1, values float32
> volume #29 level 0.07099
> volume #45 level 0.3542
> transparency #45 50
> select add #45
2 models selected
> select add #44
4198 atoms, 4031 bonds, 8 pseudobonds, 743 residues, 4 models selected
> view matrix models
> #44,-0.93556,0.2937,-0.19611,146.23,0.044071,-0.45388,-0.88997,157.07,-0.3504,-0.84127,0.41169,60.574,#45,-0.93556,0.2937,-0.19611,146.23,0.044071,-0.45388,-0.88997,157.07,-0.3504,-0.84127,0.41169,60.574
> view matrix models
> #44,-0.93556,0.2937,-0.19611,143.48,0.044071,-0.45388,-0.88997,147.76,-0.3504,-0.84127,0.41169,34.922,#45,-0.93556,0.2937,-0.19611,143.48,0.044071,-0.45388,-0.88997,147.76,-0.3504,-0.84127,0.41169,34.922
> select subtract #45
4198 atoms, 4031 bonds, 8 pseudobonds, 743 residues, 2 models selected
> select subtract #44
Nothing selected
> hide #!44 models
> select add #45
2 models selected
> view matrix models
> #45,-0.93556,0.2937,-0.19611,145.49,0.044071,-0.45388,-0.88997,159.38,-0.3504,-0.84127,0.41169,39.151
> view matrix models
> #45,-0.72949,0.54043,-0.41926,144.13,0.020765,-0.59518,-0.80333,159.59,-0.68367,-0.59473,0.42296,41.013
> view matrix models
> #45,-0.71308,0.51521,-0.47548,145.84,0.057668,-0.6328,-0.77216,158.62,-0.69871,-0.57803,0.42153,41.063
> view matrix models
> #45,-0.71308,0.51521,-0.47548,145.43,0.057668,-0.6328,-0.77216,156.8,-0.69871,-0.57803,0.42153,40.9
> view matrix models
> #45,-0.71308,0.51521,-0.47548,145.15,0.057668,-0.6328,-0.77216,154.97,-0.69871,-0.57803,0.42153,40.73
> view matrix models
> #45,-0.79988,0.54237,-0.25694,140.06,-0.020652,-0.45275,-0.8914,156.94,-0.5998,-0.70771,0.37335,42.366
> select subtract #45
Nothing selected
> show #!44 models
> fitmap #44 inMap #45
Fit molecule copy of copy of AATHNEcombined (#44) to map copy of copy of
AATHNEcombined map 6 (#45) using 4198 atoms
average map value = 0.434, steps = 72
shifted from previous position = 8.8
rotated from previous position = 16.7 degrees
atoms outside contour = 994, contour level = 0.3542
Position of copy of copy of AATHNEcombined (#44) relative to copy of copy of
AATHNEcombined map 6 (#45) coordinates:
Matrix rotation and translation
0.99999987 0.00004904 -0.00050917 0.03695210
-0.00004923 0.99999993 -0.00038442 0.00896662
0.00050915 0.00038445 0.99999980 -0.01640243
Axis 0.60079207 -0.79570876 -0.07678841
Axis point 29.77463683 0.00000000 53.30306429
Rotation angle (degrees) 0.03666236
Shift along axis 0.01632523
> select add #44
4198 atoms, 4031 bonds, 8 pseudobonds, 743 residues, 2 models selected
> view matrix models
> #44,-0.80004,0.54224,-0.25675,156.75,-0.021083,-0.45309,-0.89121,165.09,-0.59958,-0.70759,0.37392,145.97
> view matrix models
> #44,-0.80004,0.54224,-0.25675,157.44,-0.021083,-0.45309,-0.89121,165.95,-0.59958,-0.70759,0.37392,150.1
> fitmap #44 inMap #29
Fit molecule copy of copy of AATHNEcombined (#44) to map J1122.mrc (#29) using
4198 atoms
average map value = 0.08149, steps = 152
shifted from previous position = 14.4
rotated from previous position = 16.8 degrees
atoms outside contour = 2047, contour level = 0.070992
Position of copy of copy of AATHNEcombined (#44) relative to J1122.mrc (#29)
coordinates:
Matrix rotation and translation
-0.93562730 0.29338154 -0.19628760 148.35386113
0.04432994 -0.45401135 -0.88989243 165.88171301
-0.35019481 -0.84130908 0.41177983 152.48885393
Axis 0.16370521 0.51860171 -0.83919775
Axis point 96.83079976 123.33491709 0.00000000
Rotation angle (degrees) 171.46655392
Shift along axis -17.65546343
> select subtract #44
Nothing selected
> select add #45
2 models selected
> view matrix models
> #45,-0.93329,0.27115,-0.23547,146.24,0.06955,-0.50681,-0.85925,155.22,-0.35232,-0.81831,0.45414,37.269
> select subtract #45
Nothing selected
> hide #!44 models
> open /Users/amy/Downloads/cryosparc_P483_J196_007_volume_map.mrc
Opened cryosparc_P483_J196_007_volume_map.mrc as #46, grid size 400,400,400,
pixel 0.723, shown at level 0.00453, step 2, values float32
> hide #!45 models
> hide #!43 models
> hide #!29 models
> hide #!8 models
> volume #46 level 0.03417
> open /Users/amy/Downloads/cryosparc_P483_J206_005_volume_map.mrc
Opened cryosparc_P483_J206_005_volume_map.mrc as #47, grid size 400,400,400,
pixel 0.723, shown at level 0.0164, step 2, values float32
> volume #47 level 0.05223
> volume #47 level 0.05304
> volume #47 level 0.05549
> close #58-61,70-71
> show #!46 models
> hide #!46 models
> close #46-47
> show #!39 models
Error processing trigger "graphics update":
You deleted or moved a volume file that is still open in ChimeraX.
/Users/amy/Downloads/cryosparc_P483_J188_006_volume_map.mrc
To allow fast initial display of volume data ChimeraX does not read all data
from the file when it is first opened, and will later read more data when
needed. ChimeraX got an error trying to read the above file.
> close #39-40
> save "/Users/amy/Desktop/SPA AAT_HNE/csparc.cxs"
——— End of log from Thu Mar 12 17:49:41 2026 ———
> view name session-start
opened ChimeraX session
> show #!29 models
> show #!33 models
> hide #!33 models
> show #!42 models
> hide #!42 models
> open "/Users/amy/Desktop/SPA AAT_HNE/3C11_Fab_AAT_NE/model/combined.pdb"
Chain information for combined.pdb #39
---
Chain | Description
A | No description available
B | No description available
C | No description available
H | No description available
L | No description available
128 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> show #!39 cartoons
> hide #!39 atoms
> volume #29 level 0.08659
> volume #29 step 1
> volume #29 level 0.1102
> hide #!29 models
> show #!29 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> show #!39 models
> volume #29 level 0.1043
> select #39/A
2686 atoms, 2674 bonds, 398 residues, 1 model selected
> select #39/A: 75
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide #!39 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> show #!39 models
> ui tool show "Show Sequence Viewer"
> sequence chain #4/H #6/H #17/H #24/H #33/H #39/H
Alignment identifier is 1
> select #4/H:1-2 #6/H:1-2 #17/H:1-2 #24/H:1-2 #33/H:1-2 #39/H:1-2
72 atoms, 66 bonds, 12 residues, 6 models selected
> select #4/H:1-116 #6/H:1-116 #17/H:1-116 #24/H:1-116 #33/H:1-116 #39/H:1-116
5472 atoms, 5592 bonds, 708 residues, 6 models selected
Fab 3C11 Heavy Chain [ID: 1] region 6 chains [1-118] RMSD: 27.271
> select #4/H:117 #6/H:117 #17/H:117 #24/H:117 #33/H:117 #39/H:117
42 atoms, 36 bonds, 6 residues, 6 models selected
> select #4/H:117-119 #6/H:117-119 #17/H:117-119 #24/H:117-119 #33/H:117-119
> #39/H:117-119
114 atoms, 114 bonds, 18 residues, 6 models selected
Fab 3C11 Heavy Chain [ID: 1] region 6 chains [119-121] RMSD: 60.098
> select #4/H:120-121 #6/H:120-121 #17/H:120-121 #24/H:120-121 #33/H:120-121
> #39/H:120-121
78 atoms, 72 bonds, 12 residues, 6 models selected
> select #4/H:120-124 #6/H:120-124 #17/H:120-124 #24/H:120-124 #33/H:120-124
> #39/H:120-124
240 atoms, 246 bonds, 30 residues, 6 models selected
Fab 3C11 Heavy Chain [ID: 1] region 6 chains [122-126] RMSD: 70.006
> select #4/H:125 #6/H:125 #17/H:125 #24/H:125 #33/H:125 #39/H:125
30 atoms, 24 bonds, 6 residues, 6 models selected
> select #4/H:125-132 #6/H:125-132 #17/H:125-132 #24/H:125-132 #33/H:125-132
> #39/H:125-132
282 atoms, 282 bonds, 48 residues, 6 models selected
Fab 3C11 Heavy Chain [ID: 1] region 6 chains [127-135] RMSD: 85.110
> open /Applications/ccp4-9/examples/data/pdb_mmcif/input.fasta
Summary of feedback from opening
/Applications/ccp4-9/examples/data/pdb_mmcif/input.fasta
---
note | Alignment identifier is input.fasta
Opened 1 sequence from input.fasta
> select #4/H:1 #6/H:1 #17/H:1 #24/H:1 #33/H:1 #39/H:1
30 atoms, 24 bonds, 6 residues, 6 models selected
> select #4/H:1-56 #6/H:1-56 #17/H:1-56 #24/H:1-56 #33/H:1-56 #39/H:1-56
2556 atoms, 2610 bonds, 342 residues, 6 models selected
Fab 3C11 Heavy Chain [ID: 1] region 6 chains [1-57] RMSD: 25.907
> select #4/H:1 #6/H:1 #17/H:1 #24/H:1 #33/H:1 #39/H:1
30 atoms, 24 bonds, 6 residues, 6 models selected
> select #4/H:1-104 #6/H:1-104 #17/H:1-104 #24/H:1-104 #33/H:1-104 #39/H:1-104
4980 atoms, 5100 bonds, 636 residues, 6 models selected
Fab 3C11 Heavy Chain [ID: 1] region 6 chains [1-106] RMSD: 25.181
> select #4/H:1 #6/H:1 #17/H:1 #24/H:1 #33/H:1 #39/H:1
30 atoms, 24 bonds, 6 residues, 6 models selected
> select #4/H #6/H #17/H #24/H #33/H #39/H
9660 atoms, 9900 bonds, 6 pseudobonds, 1284 residues, 12 models selected
Fab 3C11 Heavy Chain [ID: 1] region 6 chains [1-215] RMSD: 48.787
> select clear
> select #4/H:1 #6/H:1 #17/H:1 #24/H:1 #33/H:1 #39/H:1
30 atoms, 24 bonds, 6 residues, 6 models selected
> select #4/H #6/H #17/H #24/H #33/H #39/H
9660 atoms, 9900 bonds, 6 pseudobonds, 1284 residues, 12 models selected
Fab 3C11 Heavy Chain [ID: 1] region 6 chains [1-215] RMSD: 48.787
> save /Users/amy/Desktop/3c11-chainA format fasta alignment 1
> ui tool show "Show Sequence Viewer"
> sequence chain #4/L #6/L #17/L #24/L #33/L #39/L
Alignment identifier is 1
> select clear
> select #4/L #6/L #17/L #24/L #33/L #39/L
9480 atoms, 9714 bonds, 6 pseudobonds, 1248 residues, 12 models selected
Fab 3C11 Light Chain [ID: 1] region 6 chains [1-215] RMSD: 54.385
> select clear
> select #4/L #6/L #17/L #24/L #33/L #39/L
9480 atoms, 9714 bonds, 6 pseudobonds, 1248 residues, 12 models selected
> select clear
> select #4/L #6/L #17/L #24/L #33/L #39/L
9480 atoms, 9714 bonds, 6 pseudobonds, 1248 residues, 12 models selected
Fab 3C11 Light Chain [ID: 1] region 6 chains [1-215] RMSD: 54.385
> save /Users/amy/Desktop/3c11-lightchain format fasta alignment 1
> open "/Users/amy/Desktop/SPA AAT_HNE/9C5_Fab_AAT_HNE/9c5_aat_hne_seq.fasta"
Failed opening file /Users/amy/Desktop/SPA
AAT_HNE/9C5_Fab_AAT_HNE/9c5_aat_hne_seq.fasta:
Sequence 'ChainB' differs in length from preceding sequences, and it is
therefore impossible to open these sequences as an alignment. If you want to
open the sequences individually, specify 'false' as the value of the
'alignment' keyword in the 'open' command.
> open /Users/amy/Downloads/J1122-fit.cif
Summary of feedback from opening /Users/amy/Downloads/J1122-fit.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for J1122-fit.cif #40
---
Chain | Description
Aa | No description available
Ab | No description available
Ba | No description available
Bb | No description available
Ca | No description available
Cb | No description available
Cc | No description available
Cd | No description available
> hide #!39 models
> hide #!40 atoms
> hide #!40 models
> show #!40 models
> show #!40 cartoons
Computing secondary structure
> open /Users/amy/Downloads/J1122-fit_raw.cif
Summary of feedback from opening /Users/amy/Downloads/J1122-fit_raw.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for J1122-fit_raw.cif #46
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
3 V X | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
8 | No description available
9 | No description available
A | No description available
A0 | No description available
A1 | No description available
A2 | No description available
A3 | No description available
A4 | No description available
A5 | No description available
A6 | No description available
A7 | No description available
A8 | No description available
A9 | No description available
AA | No description available
AB | No description available
AC | No description available
AD | No description available
AE | No description available
AF z | No description available
AG | No description available
AH An C0 C2 C9 Cl DE DS Dv Dw q | No description available
AI CY | No description available
AJ | No description available
AK | No description available
AL | No description available
AM | No description available
AN | No description available
AO | No description available
AP | No description available
AQ | No description available
AR | No description available
AS | No description available
AT | No description available
AU | No description available
AV | No description available
AW | No description available
AX | No description available
AY | No description available
AZ | No description available
Aa | No description available
Ab | No description available
Ac | No description available
Ad | No description available
Ae | No description available
Af | No description available
Ag | No description available
Ah | No description available
Ai | No description available
Aj | No description available
Ak | No description available
Al Cr Cx DP | No description available
Am | No description available
Ao | No description available
Ap | No description available
Aq | No description available
Ar | No description available
As | No description available
At | No description available
Au | No description available
Av b l | No description available
Aw | No description available
Ax | No description available
Ay BQ Bl Bm C8 CW Ce Cg Cp Cs Cu D3 D5 DC DH DL DN Dg Dh Dk Dq Dt h o | No description available
Az g r | No description available
B | No description available
B0 Ck | No description available
B1 | No description available
B2 | No description available
B3 Bw C1 DW Dj Dy S p | No description available
B4 | No description available
B5 | No description available
B6 | No description available
B7 | No description available
B8 | No description available
B9 | No description available
BA | No description available
BB | No description available
BC | No description available
BD | No description available
BE | No description available
BF | No description available
BG | No description available
BH | No description available
BI | No description available
BJ | No description available
BK | No description available
BL | No description available
BM | No description available
BN | No description available
BO | No description available
BP | No description available
BR | No description available
BS | No description available
BT D4 Dp | No description available
BU | No description available
BV | No description available
BW | No description available
BX | No description available
BY | No description available
BZ | No description available
Ba | No description available
Bb | No description available
Bc | No description available
Bd | No description available
Be | No description available
Bf | No description available
Bg | No description available
Bh | No description available
Bi | No description available
Bj | No description available
Bk | No description available
Bn | No description available
Bo | No description available
Bp | No description available
Bq e | No description available
Br | No description available
Bs | No description available
Bt | No description available
Bu | No description available
Bv | No description available
Bx | No description available
By | No description available
Bz | No description available
C | No description available
C3 | No description available
C4 | No description available
C5 | No description available
C6 Cv D0 | No description available
C7 | No description available
CA | No description available
CB | No description available
CC | No description available
CD | No description available
CE | No description available
CF | No description available
CG | No description available
CH | No description available
CI | No description available
CJ | No description available
CK | No description available
CL | No description available
CM | No description available
CN | No description available
CO | No description available
CP | No description available
CQ | No description available
CR | No description available
CS | No description available
CT | No description available
CU | No description available
CV | No description available
CX | No description available
CZ Cz D6 DF Da De Df j | No description available
Ca k | No description available
Cb DA Ds | No description available
Cc | No description available
Cd | No description available
Cf Dm | No description available
Ch | No description available
Ci DQ | No description available
Cj | No description available
Cm | No description available
Cn | No description available
Co DB Dd | No description available
Cq Dr | No description available
Ct DM | No description available
Cw | No description available
Cy | No description available
D | No description available
D1 | No description available
D2 Dz W | No description available
D7 | No description available
DD | No description available
DG | No description available
DI | No description available
DJ | No description available
DK | No description available
DO | No description available
DR | No description available
DT | No description available
DU | No description available
DV | No description available
DX Db | No description available
DY | No description available
DZ | No description available
Dc | No description available
Di Dl Do | No description available
Dn | No description available
Du | No description available
Dx | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
T | No description available
U | No description available
Y | No description available
Z | No description available
a | No description available
c | No description available
d | No description available
f | No description available
i y | No description available
m | No description available
n | No description available
s | No description available
t | No description available
u | No description available
v | No description available
w | No description available
x | No description available
> hide #46#!40 atoms
> show #46#!40 cartoons
Computing secondary structure
> hide #!40 models
> hide #!29 models
> show #!29 models
> hide #!29 models
> show #!29 models
> hide #46 models
> show #!39 models
> select add #39
15863 atoms, 15994 bonds, 7 pseudobonds, 2296 residues, 12 models selected
> select subtract #39
7900 atoms, 8095 bonds, 5 pseudobonds, 1040 residues, 10 models selected
> hide #!39 cartoons
> show #!39 atoms
> hide #!39 atoms
> show #!39 atoms
> style #!39 stick
Changed 7963 atom styles
> select #39/A: 39
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #39/A: 305
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel byhetero
> select #39/H: 96
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel byhetero
> select add #39
7963 atoms, 7899 bonds, 2 pseudobonds, 1256 residues, 2 models selected
> select subtract #39
Nothing selected
> select add #39
7963 atoms, 7899 bonds, 2 pseudobonds, 1256 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> select subtract #39
Nothing selected
> select add #39
7963 atoms, 7899 bonds, 2 pseudobonds, 1256 residues, 2 models selected
> ui tool show "Fit in Map"
> fitmap #39 inMap #29
Fit molecule combined.pdb (#39) to map J1122.mrc (#29) using 7963 atoms
average map value = 0.08036, steps = 68
shifted from previous position = 0.771
rotated from previous position = 2.19 degrees
atoms outside contour = 5609, contour level = 0.10431
Position of combined.pdb (#39) relative to J1122.mrc (#29) coordinates:
Matrix rotation and translation
0.99967761 0.02538913 0.00025294 -3.33021005
-0.02538599 0.99926934 0.02857152 0.48178557
0.00047265 -0.02856873 0.99959172 3.88702701
Axis -0.74751146 -0.00287429 -0.66424269
Axis point 0.00000000 134.06640595 -13.42452344
Rotation angle (degrees) 2.19039607
Shift along axis -0.09394389
> select subtract #39
Nothing selected
> volume #29 level 0.1191
> style #!39 stick
Changed 7963 atom styles
> hide #!39 cartoons
> show #!39 atoms
> nucleotides #!39 atoms
> style nucleic & #!39 stick
Changed 0 atom styles
> nucleotides #!39 atoms
> style nucleic & #!39 stick
Changed 0 atom styles
> nucleotides #!39 atoms
> style nucleic & #!39 stick
Changed 0 atom styles
> hide #!39 atoms
> show #!39 atoms
> nucleotides #!39 ladder
> nucleotides #!39 fill
> style nucleic & #!39 stick
Changed 0 atom styles
> nucleotides #!39 tube/slab shape box
> nucleotides #!39 ladder
> hbonds #!39 reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 8pi2 #35/A ARG 101 NE
13841 hydrogen bonds found
> interfaces #!39 & ~solvent
5 buried areas: A C 2439, H L 1779, A H 684, A B 593, B L 433
> select #39/A:32@CB
1 atom, 1 residue, 1 model selected
> select clear
> select #39/H: 32
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #39/A: 32
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel byhetero
> select #39/H: 28
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel byhetero
> distance #39/A:32 #39/H:28
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or
one or more measurable objects and one or more atoms, got 16 atoms and 0
measurable objects
> distance #39/A:32@OE1 #39/H:28@OG1
Distance between combined.pdb #39/A GLU 32 OE1 and /H THR 28 OG1: 3.567Å
> select up
48 atoms, 49 bonds, 5 residues, 1 model selected
> select up
1018 atoms, 1042 bonds, 134 residues, 1 model selected
> select down
48 atoms, 49 bonds, 5 residues, 1 model selected
> select down
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #39/A: 75
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel byhetero
> select #39/H: 56
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel byhetero
> distance #39/A:75@OE2 #39/H:56@OG
Distance between combined.pdb #39/A GLU 75 OE2 and /H SER 56 OG: 2.495Å
> select #39/A: 36
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #39/A: 306
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #39/A: 302
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #39/A: 2
Nothing selected
> select #39/A: 32
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #39/A: 36
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #39
7963 atoms, 7899 bonds, 1523 pseudobonds, 1256 residues, 4 models selected
> select subtract #39
Nothing selected
> select add #39
7963 atoms, 7899 bonds, 1523 pseudobonds, 1256 residues, 4 models selected
> show sel cartoons
> hide sel atoms
> hide sel cartoons
> show sel atoms
> hide sel cartoons
> hide sel atoms
> show sel cartoons
> ui tool show "Show Sequence Viewer"
> sequence chain #4/H #6/H #17/H #24/H #33/H #39/H
Alignment identifier is 1
> select clear
> select #4/H:1 #6/H:1 #17/H:1 #24/H:1 #33/H:1 #39/H:1
30 atoms, 24 bonds, 6 residues, 6 models selected
> select #4/H:1-169 #6/H:1-169 #17/H:1-169 #24/H:1-169 #33/H:1-169 #39/H:1-169
7686 atoms, 7878 bonds, 341 pseudobonds, 1020 residues, 13 models selected
Fab 3C11 Heavy Chain [ID: 1] region 6 chains [1-171] RMSD: 42.741
> select #4/H:213 #6/H:213 #17/H:213 #24/H:213 #33/H:213 #39/H:213
72 atoms, 66 bonds, 6 residues, 6 models selected
> select #4/H:151-213 #6/H:151-213 #17/H:151-213 #24/H:151-213 #33/H:151-213
> #39/H:151-213
2802 atoms, 2868 bonds, 149 pseudobonds, 378 residues, 7 models selected
Fab 3C11 Heavy Chain [ID: 1] region 6 chains [153-215] RMSD: 64.253
> select #4/H:1-2 #6/H:1-2 #17/H:1-2 #24/H:1-2 #33/H:1-2 #39/H:1-2
72 atoms, 66 bonds, 12 residues, 6 models selected
> select #4/H:1-146 #6/H:1-146 #17/H:1-146 #24/H:1-146 #33/H:1-146 #39/H:1-146
6678 atoms, 6828 bonds, 312 pseudobonds, 882 residues, 13 models selected
Fab 3C11 Heavy Chain [ID: 1] region 6 chains [1-148] RMSD: 40.342
> select #4/H:1 #6/H:1 #17/H:1 #24/H:1 #33/H:1 #39/H:1
30 atoms, 24 bonds, 6 residues, 6 models selected
> select #4/H:1-140 #6/H:1-140 #17/H:1-140 #24/H:1-140 #33/H:1-140 #39/H:1-140
6372 atoms, 6510 bonds, 303 pseudobonds, 846 residues, 13 models selected
Fab 3C11 Heavy Chain [ID: 1] region 6 chains [1-142] RMSD: 39.273
> select #4/H:1-2 #6/H:1-2 #17/H:1-2 #24/H:1-2 #33/H:1-2 #39/H:1-2
72 atoms, 66 bonds, 12 residues, 6 models selected
> select #4/H:1-132 #6/H:1-132 #17/H:1-132 #24/H:1-132 #33/H:1-132 #39/H:1-132
6108 atoms, 6252 bonds, 279 pseudobonds, 804 residues, 7 models selected
Fab 3C11 Heavy Chain [ID: 1] region 6 chains [1-134] RMSD: 36.760
> select #4/H:1 #6/H:1 #17/H:1 #24/H:1 #33/H:1 #39/H:1
30 atoms, 24 bonds, 6 residues, 6 models selected
> select #4/H:1-128 #6/H:1-128 #17/H:1-128 #24/H:1-128 #33/H:1-128 #39/H:1-128
5976 atoms, 6120 bonds, 277 pseudobonds, 780 residues, 7 models selected
Fab 3C11 Heavy Chain [ID: 1] region 6 chains [1-130] RMSD: 33.946
> select #4/H:1-2 #6/H:1-2 #17/H:1-2 #24/H:1-2 #33/H:1-2 #39/H:1-2
72 atoms, 66 bonds, 12 residues, 6 models selected
> select #4/H:1-94 #6/H:1-94 #17/H:1-94 #24/H:1-94 #33/H:1-94 #39/H:1-94
4548 atoms, 4644 bonds, 204 pseudobonds, 588 residues, 7 models selected
Fab 3C11 Heavy Chain [ID: 1] region 6 chains [1-98] RMSD: 25.989
> select #4/H:1-101 #6/H:1-101 #17/H:1-101 #24/H:1-101 #33/H:1-101 #39/H:1-101
4806 atoms, 4908 bonds, 222 pseudobonds, 618 residues, 7 models selected
Fab 3C11 Heavy Chain [ID: 1] region 6 chains [1-98] + 1 other block RMSD:
25.402
> select #4/H:1-106 #6/H:1-106 #17/H:1-106 #24/H:1-106 #33/H:1-106 #39/H:1-106
5058 atoms, 5178 bonds, 235 pseudobonds, 648 residues, 7 models selected
Fab 3C11 Heavy Chain [ID: 1] region 6 chains [1-98] + 2 other blocks RMSD:
25.227
> select #4/H:1-111 #6/H:1-111 #17/H:1-111 #24/H:1-111 #33/H:1-111 #39/H:1-111
5274 atoms, 5394 bonds, 258 pseudobonds, 678 residues, 7 models selected
Fab 3C11 Heavy Chain [ID: 1] region 6 chains [1-98] + 3 other blocks RMSD:
25.743
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #4/L #6/L #17/L #24/L #33/L #39/L
Alignment identifier is 1
> select #4/L:2 #6/L:2 #17/L:2 #24/L:2 #33/L:2 #39/L:2
48 atoms, 42 bonds, 6 residues, 6 models selected
> select #4/L:2-113 #6/L:2-113 #17/L:2-113 #24/L:2-113 #33/L:2-113 #39/L:2-113
4782 atoms, 4896 bonds, 292 pseudobonds, 636 residues, 13 models selected
Fab 3C11 Light Chain [ID: 1] region 6 chains [1-113] RMSD: 28.868
> select #4/L:2-113 #6/L:2-113 #17/L:2-113 #24/L:2-113 #33/L:2-113 #39/L:2-113
4782 atoms, 4896 bonds, 292 pseudobonds, 636 residues, 13 models selected
Fab 3C11 Light Chain [ID: 1] region 6 chains [1-113] + 1 other block RMSD:
30.988
> select clear
> select #4/L:2-97 #6/L:2-97 #17/L:2-97 #24/L:2-97 #33/L:2-97 #39/L:2-97
4128 atoms, 4236 bonds, 234 pseudobonds, 540 residues, 13 models selected
Fab 3C11 Light Chain [ID: 1] region 6 chains [1-97] RMSD: 25.885
> select #4/L:2-97,100-102 #6/L:2-97,100-102 #17/L:2-97,100-102
> #24/L:2-97,100-102 #33/L:2-97,100-102 #39/L:2-97,100-102
4200 atoms, 4302 bonds, 241 pseudobonds, 558 residues, 13 models selected
Fab 3C11 Light Chain [ID: 1] region 6 chains [1-97] + 1 other block RMSD:
25.843
> select #4/L:2-102 #6/L:2-102 #17/L:2-102 #24/L:2-102 #33/L:2-102 #39/L:2-102
4308 atoms, 4422 bonds, 261 pseudobonds, 570 residues, 13 models selected
Fab 3C11 Light Chain [ID: 1] region 6 chains [1-97] + 2 other blocks RMSD:
25.676
> select #4/L:2-102 #6/L:2-102 #17/L:2-102 #24/L:2-102 #33/L:2-102 #39/L:2-102
4308 atoms, 4422 bonds, 261 pseudobonds, 570 residues, 13 models selected
Fab 3C11 Light Chain [ID: 1] region 6 chains [1-97] + 3 other blocks RMSD:
25.676
> select clear
> select #4/L:80-84,122-128,184-188 #6/L:80-84,122-128,184-188
> #17/L:80-84,122-128,184-188 #24/L:80-84,122-128,184-188
> #33/L:80-84,122-128,184-188 #39/L:80-84,122-128,184-188
834 atoms, 828 bonds, 39 pseudobonds, 102 residues, 7 models selected
> select
> #4/L:5-6,11-14,20-26,33-39,46-52,63-68,71-76,85-91,98-99,103-107,115-119,130-140,146-151,154-156,160-164,174-183,192-198,206-211
> #6/L:5-6,11-14,20-26,33-39,46-52,63-68,71-76,85-91,98-99,103-107,115-119,130-140,146-151,154-156,160-164,174-183,192-198,206-211
> #17/L:5-6,11-14,20-26,33-39,46-52,63-68,71-76,85-91,98-99,103-107,115-119,130-140,146-151,154-156,160-164,174-183,192-198,206-211
> #24/L:5-6,11-14,20-26,33-39,46-52,63-68,71-76,85-91,98-99,103-107,115-119,130-140,146-151,154-156,160-164,174-183,192-198,206-211
> #33/L:5-6,11-14,20-26,33-39,46-52,63-68,71-76,85-91,98-99,103-107,115-119,130-140,146-151,154-156,160-164,174-183,192-198,206-211
> #39/L:5-6,11-14,20-26,33-39,46-52,63-68,71-76,85-91,98-99,103-107,115-119,130-140,146-151,154-156,160-164,174-183,192-198,206-211
4968 atoms, 4998 bonds, 292 pseudobonds, 636 residues, 7 models selected
> select clear
> select #4/L:2-102 #6/L:2-102 #17/L:2-102 #24/L:2-102 #33/L:2-102 #39/L:2-102
4308 atoms, 4422 bonds, 261 pseudobonds, 570 residues, 13 models selected
Fab 3C11 Light Chain [ID: 1] region 6 chains [1-102] RMSD: 25.676
> select #4/L:2-107 #6/L:2-107 #17/L:2-107 #24/L:2-107 #33/L:2-107 #39/L:2-107
4530 atoms, 4644 bonds, 286 pseudobonds, 600 residues, 13 models selected
Fab 3C11 Light Chain [ID: 1] region 6 chains [1-102] + 1 other block RMSD:
26.293
> open /Users/amy/Downloads/J1122_fit2.cif
Summary of feedback from opening /Users/amy/Downloads/J1122_fit2.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for J1122_fit2.cif #49
---
Chain | Description
Aa | No description available
Ab | No description available
Ac | No description available
Ad | No description available
Ae | No description available
Ba | No description available
Bb | No description available
Bc | No description available
Ca | No description available
Cb | No description available
Cc | No description available
> open /Users/amy/Downloads/J1122_fit2_raw.cif
Summary of feedback from opening /Users/amy/Downloads/J1122_fit2_raw.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for J1122_fit2_raw.cif #50
---
Chain | Description
0 5 BM CZ Co Cp Cy D4 DK DL DT DY DZ Dd Dk Do Dq EA U y | No description available
1 | No description available
2 A7 | No description available
3 t | No description available
4 x | No description available
6 | No description available
7 BF C5 Cj Cl Cn Cq D9 DP DQ Da Dm | No description available
8 | No description available
9 D8 | No description available
A | No description available
A0 | No description available
A1 | No description available
A2 | No description available
A3 AR Al | No description available
A4 | No description available
A5 | No description available
A6 | No description available
A8 r | No description available
A9 | No description available
AA | No description available
AB C7 | No description available
AC u | No description available
AD | No description available
AE An BA | No description available
AF | No description available
AG | No description available
AH | No description available
AI | No description available
AJ | No description available
AK DO | No description available
AL | No description available
AM | No description available
AN | No description available
AO | No description available
AP DD | No description available
AQ | No description available
AS | No description available
AT | No description available
AU | No description available
AV | No description available
AW | No description available
AX | No description available
AY | No description available
AZ | No description available
Aa | No description available
Ab | No description available
Ac | No description available
Ad | No description available
Ae | No description available
Af | No description available
Ag | No description available
Ah | No description available
Ai | No description available
Aj Ch Cw | No description available
Ak | No description available
Am | No description available
Ao | No description available
Ap | No description available
Aq | No description available
Ar | No description available
As | No description available
At | No description available
Au DS | No description available
Av | No description available
Aw Ck | No description available
Ax Ci | No description available
Ay | No description available
Az | No description available
B | No description available
B0 | No description available
B1 | No description available
B2 | No description available
B3 | No description available
B4 | No description available
B5 | No description available
B6 | No description available
B7 | No description available
B8 | No description available
B9 | No description available
BB | No description available
BC | No description available
BD | No description available
BE | No description available
BG | No description available
BH | No description available
BI | No description available
BJ | No description available
BK | No description available
BL | No description available
BN | No description available
BO | No description available
BP | No description available
BQ | No description available
BR | No description available
BS | No description available
BT | No description available
BU | No description available
BV | No description available
BW | No description available
BX | No description available
BY | No description available
BZ | No description available
Ba | No description available
Bb | No description available
Bc | No description available
Bd | No description available
Be | No description available
Bf | No description available
Bg | No description available
Bh | No description available
Bi | No description available
Bj | No description available
Bk | No description available
Bl | No description available
Bm | No description available
Bn | No description available
Bo DA DE DR Dh Dw Dz | No description available
Bp | No description available
Bq | No description available
Br | No description available
Bs | No description available
Bt | No description available
Bu | No description available
Bv | No description available
Bw | No description available
Bx | No description available
By | No description available
Bz | No description available
C | No description available
C0 C1 C2 Cr Ct Cv Cx DF DU DW Dl Dr Ds Dx s | No description available
C3 | No description available
C4 D3 | No description available
C6 D0 D5 | No description available
C8 | No description available
C9 DX | No description available
CA | No description available
CB | No description available
CC | No description available
CD | No description available
CE | No description available
CF | No description available
CG | No description available
CH | No description available
CI | No description available
CJ | No description available
CK | No description available
CL | No description available
CM | No description available
CN | No description available
CO | No description available
CP | No description available
CQ | No description available
CR | No description available
CS | No description available
CT | No description available
CU | No description available
CV | No description available
CW | No description available
CX | No description available
CY | No description available
Ca Cc D7 DV l | No description available
Cb | No description available
Cd Di Dt | No description available
Ce Df | No description available
Cf DJ Du | No description available
Cg | No description available
Cm | No description available
Cs Dc | No description available
Cu | No description available
Cz DI | No description available
D | No description available
D1 DH | No description available
D2 DB | No description available
D6 | No description available
DC Z | No description available
DG | No description available
DM | No description available
DN | No description available
Db | No description available
De | No description available
Dg | No description available
Dj | No description available
Dn | No description available
Dp | No description available
Dv | No description available
Dy | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
V | No description available
W p | No description available
X | No description available
Y | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
m | No description available
n | No description available
o | No description available
q | No description available
v | No description available
w | No description available
z | No description available
> hide sel & #!39 atoms
> show sel & #!39 cartoons
> hide sel & #!39 surfaces
> hide sel & #!39 atoms
> hide sel & #!39 cartoons
> show sel & #!39 cartoons
> select add #33
6965 atoms, 7140 bonds, 287 pseudobonds, 922 residues, 14 models selected
> select subtract #33
3775 atoms, 3870 bonds, 274 pseudobonds, 500 residues, 11 models selected
> select clear
> hide #50#!39,49 atoms
> show #50#!39,49 cartoons
Computing secondary structure
> hide #!39 models
> hide #50 models
> show #50 models
> hide #!49 models
> show #50 atoms
> style #50 stick
Changed 9637 atom styles
> hide #50 cartoons
> hbonds #50 reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 8pi2 #35/A ARG 101 NE
12126 hydrogen bonds found
> select #29
2 models selected
> select #29
2 models selected
> select clear
> select #50/H: 23
10 atoms, 10 bonds, 1 residue, 1 model selected
> color sel byhetero
> select #50/CR: 3
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel byhetero
> distance #50/H:23@O 50£/CR:3@ND2
Expected a keyword
> distance #50/H:23@O #50/CR:3@ND2
Distance between J1122_fit2_raw.cif #50/H HIS 23 O and /CR ASN 3 ND2: 2.742Å
> show #!39 models
> hide #50 models
> show #!39 atoms
> hide #!39 cartoons
> show #50 models
> hide #50 models
> show #50 models
> ui tool show "Show Sequence Viewer"
> sequence chain #4/L #6/L #17/L #24/L #33/L #39/L
Alignment identifier is 2
> hide #50 models
> show #50 models
> hide #50 models
> select
> #4/L:5-6,11-14,20-26,33-39,46-52,63-68,71-76,85-91,98-99,103-107,115-119,130-140,146-151,154-156,160-164,174-183,192-198,206-211
> #6/L:5-6,11-14,20-26,33-39,46-52,63-68,71-76,85-91,98-99,103-107,115-119,130-140,146-151,154-156,160-164,174-183,192-198,206-211
> #17/L:5-6,11-14,20-26,33-39,46-52,63-68,71-76,85-91,98-99,103-107,115-119,130-140,146-151,154-156,160-164,174-183,192-198,206-211
> #24/L:5-6,11-14,20-26,33-39,46-52,63-68,71-76,85-91,98-99,103-107,115-119,130-140,146-151,154-156,160-164,174-183,192-198,206-211
> #33/L:5-6,11-14,20-26,33-39,46-52,63-68,71-76,85-91,98-99,103-107,115-119,130-140,146-151,154-156,160-164,174-183,192-198,206-211
> #39/L:5-6,11-14,20-26,33-39,46-52,63-68,71-76,85-91,98-99,103-107,115-119,130-140,146-151,154-156,160-164,174-183,192-198,206-211
4968 atoms, 4998 bonds, 636 residues, 6 models selected
> select clear
> select #4/L:32-33 #6/L:32-33 #17/L:32-33 #24/L:32-33 #33/L:32-33 #39/L:32-33
96 atoms, 90 bonds, 12 residues, 6 models selected
> select #4/L:32-33 #6/L:32-33 #17/L:32-33 #24/L:32-33 #33/L:32-33 #39/L:32-33
96 atoms, 90 bonds, 12 residues, 6 models selected
Fab 3C11 Light Chain [ID: 2] region 6 chains [32-33] RMSD: 11.231
> show #50 models
> select clear
> select #4/L #6/L #17/L #24/L #33/L #39/L
9480 atoms, 9714 bonds, 6 pseudobonds, 1248 residues, 12 models selected
Fab 3C11 Light Chain [ID: 2] region 6 chains [1-215] RMSD: 54.353
> save /Users/amy/Desktop/lightchain format fasta alignment 2
> select clear
> hide #!39 models
> hide #50 models
> show #!49 models
> hide #!49 cartoons
> show #!49 atoms
> hide #!49 cartoons
> style #!49 stick
Changed 1939 atom styles
> hbonds #!49 reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 8pi2 #35/A ARG 101 NE
3318 hydrogen bonds found
> sequence chain
> #1/A#5/A#16/A#19/A#23/A#26/A#31/A#32/A#37/A#42/C#43/C#44/C#39/A
Alignment identifier is 3
> sequence chain
> #1/B#5/B#16/B#19/B#23/B#26/B#31/B#32/B#37/B#42/B#43/B#44/B#39/C
Alignment identifier is 4
> sequence chain #4/H#6/H#17/H#24/H#33/H#39/H
Alignment identifier is 5
> sequence chain #4/L#6/L#17/L#24/L#33/L#39/L
Alignment identifier is 6
> sequence chain #7/A#18/A#20/A#25/A#42/A#43/A#44/A
Alignment identifier is 7
> sequence chain #19/C#26/C#32/C#30/B#37/C#57/C
Alignment identifier is 8
> sequence chain #27/B#36/B#39/B
Alignment identifier is 9
> sequence chain #35/A
Alignment identifier is 35/A
> sequence chain #36/A
Alignment identifier is 36/A
> sequence chain #38/A
Alignment identifier is 38/A
> sequence chain #38/B
Alignment identifier is 38/B
> sequence chain #38/H
Alignment identifier is 38/H
> sequence chain #38/L
Alignment identifier is 38/L
> sequence chain #40/Ba
Alignment identifier is 40/Ba
> sequence chain #40/Ca
Alignment identifier is 40/Ca
> sequence chain #40/Aa
Alignment identifier is 40/Aa
> sequence chain #40/Bb
Alignment identifier is 40/Bb
> sequence chain #40/Ab
Alignment identifier is 40/Ab
> sequence chain #40/Cb
Alignment identifier is 40/Cb
> sequence chain #40/Cc
Alignment identifier is 40/Cc
> sequence chain #40/Cd
Alignment identifier is 40/Cd
> sequence chain #46/A
Alignment identifier is 46/A
> sequence chain #46/B
Alignment identifier is 46/B
> sequence chain #46/C
Alignment identifier is 46/C
> sequence chain #46/D
Alignment identifier is 46/D
> sequence chain #46/E
Alignment identifier is 46/E
> sequence chain #46/F
Alignment identifier is 46/F
> sequence chain #46/G
Alignment identifier is 46/G
> sequence chain #46/H
Alignment identifier is 46/H
> sequence chain #46/I
Alignment identifier is 46/I
> sequence chain #46/J
Alignment identifier is 46/J
> sequence chain #46/K
Alignment identifier is 46/K
> sequence chain #46/L
Alignment identifier is 46/L
> sequence chain #46/M
Alignment identifier is 46/M
> sequence chain #46/N
Alignment identifier is 46/N
> sequence chain #46/O
Alignment identifier is 46/O
> sequence chain #46/P
Alignment identifier is 46/P
> sequence chain #46/Q
Alignment identifier is 46/Q
> sequence chain #46/R#50/j
Alignment identifier is 10
> sequence chain #46/S,p,Bw,B3,C1,DW,Dj,Dy#50/Bo,DA,DE,DR,Dh,Dw,Dz
Alignment identifier is 11
> sequence chain #46/T#50/Ag
Alignment identifier is 12
> sequence chain #46/U
Alignment identifier is 46/U
> sequence chain #46/V,X,3
Alignment identifier is 13
> sequence chain #46/W,Dz,D2#50/Ay
Alignment identifier is 14
> sequence chain #46/Y
Alignment identifier is 46/Y
> sequence chain #46/Z
Alignment identifier is 46/Z
> sequence chain #46/a
Alignment identifier is 46/a
> sequence chain #46/b,l,Av#50/a
Alignment identifier is 15
> sequence chain #46/c
Alignment identifier is 46/c
> sequence chain #46/d
Alignment identifier is 46/d
> sequence chain #46/e,Bq#50/u,AC
Alignment identifier is 16
> sequence chain #46/f
Alignment identifier is 46/f
> sequence chain #46/g,r,Az
Alignment identifier is 17
> sequence chain
> #46/h,o,Ay,BQ,Bl,Bm,CW,Ce,Cg,Cp,Cs,Cu,C8,DC,DH,DL,DN,Dg,Dh,Dk,Dq,Dt,D3,D5#50/U,y,0,5,BM,CZ,Co,Cp,Cy,DK,DL,DT,DY,DZ,Dd,Dk,Do,Dq,D4,EA
Alignment identifier is 18
> sequence chain #46/i,y
Alignment identifier is 19
> sequence chain
> #46/j,CZ,Cz,DF,Da,De,Df,D6#50/7,BF,Cj,Cl,Cn,Cq,C5,DP,DQ,Da,Dm,D9
Alignment identifier is 20
> sequence chain #46/k,Ca
Alignment identifier is 21
> sequence chain #46/m
Alignment identifier is 46/m
> sequence chain #46/n
Alignment identifier is 46/n
> sequence chain
> #46/q,AH,An,Cl,C0,C2,C9,DE,DS,Dv,Dw#50/s,Cr,Ct,Cv,Cx,C0,C1,C2,DF,DU,DW,Dl,Dr,Ds,Dx
Alignment identifier is 22
> sequence chain #46/s
Alignment identifier is 46/s
> sequence chain #46/t
Alignment identifier is 46/t
> sequence chain #46/u
Alignment identifier is 46/u
> sequence chain #46/v
Alignment identifier is 46/v
> sequence chain #46/w
Alignment identifier is 46/w
> sequence chain #46/x
Alignment identifier is 46/x
> sequence chain #46/z,AF#50/6
Alignment identifier is 23
> sequence chain #46/0
Alignment identifier is 46/0
> sequence chain #46/1
Alignment identifier is 46/1
> sequence chain #46/2
Alignment identifier is 46/2
> sequence chain #46/4
Alignment identifier is 46/4
> sequence chain #46/5
Alignment identifier is 46/5
> sequence chain #46/6
Alignment identifier is 46/6
> sequence chain #46/7
Alignment identifier is 46/7
> sequence chain #46/8
Alignment identifier is 46/8
> sequence chain #46/9
Alignment identifier is 46/9
> sequence chain #46/AA
Alignment identifier is 46/AA
> sequence chain #46/AB
Alignment identifier is 46/AB
> sequence chain #46/AC
Alignment identifier is 46/AC
> sequence chain #46/AD
Alignment identifier is 46/AD
> sequence chain #46/AE#50/AZ
Alignment identifier is 24
> sequence chain #46/AG
Alignment identifier is 46/AG
> sequence chain #46/AI,CY#50/Cf,DJ,Du
Alignment identifier is 25
> sequence chain #46/AJ
Alignment identifier is 46/AJ
> sequence chain #46/AK
Alignment identifier is 46/AK
> sequence chain #46/AL
Alignment identifier is 46/AL
> sequence chain #46/AM
Alignment identifier is 46/AM
> sequence chain #46/AN
Alignment identifier is 46/AN
> sequence chain #46/AO
Alignment identifier is 46/AO
> sequence chain #46/AP
Alignment identifier is 46/AP
> sequence chain #46/AQ
Alignment identifier is 46/AQ
> sequence chain #46/AR
Alignment identifier is 46/AR
> sequence chain #46/AS
Alignment identifier is 46/AS
> sequence chain #46/AT
Alignment identifier is 46/AT
> sequence chain #46/AU
Alignment identifier is 46/AU
> sequence chain #46/AV
Alignment identifier is 46/AV
> sequence chain #46/AW
Alignment identifier is 46/AW
> sequence chain #46/AX
Alignment identifier is 46/AX
> sequence chain #46/AY
Alignment identifier is 46/AY
> sequence chain #46/AZ
Alignment identifier is 46/AZ
> sequence chain #46/Aa
Alignment identifier is 46/Aa
> sequence chain #46/Ab
Alignment identifier is 46/Ab
> sequence chain #46/Ac
Alignment identifier is 46/Ac
> sequence chain #46/Ad
Alignment identifier is 46/Ad
> sequence chain #46/Ae
Alignment identifier is 46/Ae
> sequence chain #46/Af
Alignment identifier is 46/Af
> sequence chain #46/Ag
Alignment identifier is 46/Ag
> sequence chain #46/Ah
Alignment identifier is 46/Ah
> sequence chain #46/Ai
Alignment identifier is 46/Ai
> sequence chain #46/Aj
Alignment identifier is 46/Aj
> sequence chain #46/Ak
Alignment identifier is 46/Ak
> sequence chain #46/Al,Cr,Cx,DP#50/Cm
Alignment identifier is 26
> sequence chain #46/Am#50/C4,D3
Alignment identifier is 27
> sequence chain #46/Ao
Alignment identifier is 46/Ao
> sequence chain #46/Ap
Alignment identifier is 46/Ap
> sequence chain #46/Aq
Alignment identifier is 46/Aq
> sequence chain #46/Ar
Alignment identifier is 46/Ar
> sequence chain #46/As
Alignment identifier is 46/As
> sequence chain #46/At
Alignment identifier is 46/At
> sequence chain #46/Au
Alignment identifier is 46/Au
> sequence chain #46/Aw
Alignment identifier is 46/Aw
> sequence chain #46/Ax
Alignment identifier is 46/Ax
> sequence chain #46/A0
Alignment identifier is 46/A0
> sequence chain #46/A1
Alignment identifier is 46/A1
> sequence chain #46/A2#50/AR,Al,A3
Alignment identifier is 28
> sequence chain #46/A3
Alignment identifier is 46/A3
> sequence chain #46/A4#50/A1
Alignment identifier is 29
> sequence chain #46/A5
Alignment identifier is 46/A5
> sequence chain #46/A6#50/v
Alignment identifier is 30
> sequence chain #46/A7
Alignment identifier is 46/A7
> sequence chain #46/A8
Alignment identifier is 46/A8
> sequence chain #46/A9
Alignment identifier is 46/A9
> sequence chain #46/BA
Alignment identifier is 46/BA
> sequence chain #46/BB
Alignment identifier is 46/BB
> sequence chain #46/BC
Alignment identifier is 46/BC
> sequence chain #46/BD
Alignment identifier is 46/BD
> sequence chain #46/BE
Alignment identifier is 46/BE
> sequence chain #46/BF
Alignment identifier is 46/BF
> sequence chain #46/BG
Alignment identifier is 46/BG
> sequence chain #46/BH
Alignment identifier is 46/BH
> sequence chain #46/BI
Alignment identifier is 46/BI
> sequence chain #46/BJ
Alignment identifier is 46/BJ
> sequence chain #46/BK
Alignment identifier is 46/BK
> sequence chain #46/BL
Alignment identifier is 46/BL
> sequence chain #46/BM
Alignment identifier is 46/BM
> sequence chain #46/BN
Alignment identifier is 46/BN
> sequence chain #46/BO
Alignment identifier is 46/BO
> sequence chain #46/BP
Alignment identifier is 46/BP
> sequence chain #46/BR
Alignment identifier is 46/BR
> sequence chain #46/BS
Alignment identifier is 46/BS
> sequence chain #46/BT,Dp,D4#50/DH,D1
Alignment identifier is 31
> sequence chain #46/BU
Alignment identifier is 46/BU
> sequence chain #46/BV
Alignment identifier is 46/BV
> sequence chain #46/BW
Alignment identifier is 46/BW
> sequence chain #46/BX
Alignment identifier is 46/BX
> sequence chain #46/BY
Alignment identifier is 46/BY
> sequence chain #46/BZ
Alignment identifier is 46/BZ
> sequence chain #46/Ba
Alignment identifier is 46/Ba
> sequence chain #46/Bb
Alignment identifier is 46/Bb
> sequence chain #46/Bc
Alignment identifier is 46/Bc
> sequence chain #46/Bd
Alignment identifier is 46/Bd
> sequence chain #46/Be
Alignment identifier is 46/Be
> sequence chain #46/Bf
Alignment identifier is 46/Bf
> sequence chain #46/Bg
Alignment identifier is 46/Bg
> sequence chain #46/Bh
Alignment identifier is 46/Bh
> sequence chain #46/Bi
Alignment identifier is 46/Bi
> sequence chain #46/Bj
Alignment identifier is 46/Bj
> sequence chain #46/Bk
Alignment identifier is 46/Bk
> sequence chain #46/Bn
Alignment identifier is 46/Bn
> sequence chain #46/Bo
Alignment identifier is 46/Bo
> sequence chain #46/Bp
Alignment identifier is 46/Bp
> sequence chain #46/Br
Alignment identifier is 46/Br
> sequence chain #46/Bs
Alignment identifier is 46/Bs
> sequence chain #46/Bt
Alignment identifier is 46/Bt
> sequence chain #46/Bu
Alignment identifier is 46/Bu
> sequence chain #46/Bv
Alignment identifier is 46/Bv
> sequence chain #46/Bx
Alignment identifier is 46/Bx
> sequence chain #46/By
Alignment identifier is 46/By
> sequence chain #46/Bz
Alignment identifier is 46/Bz
> sequence chain #46/B0,Ck#50/C3
Alignment identifier is 32
> sequence chain #46/B1
Alignment identifier is 46/B1
> sequence chain #46/B2
Alignment identifier is 46/B2
> sequence chain #46/B4
Alignment identifier is 46/B4
> sequence chain #46/B5
Alignment identifier is 46/B5
> sequence chain #46/B6
Alignment identifier is 46/B6
> sequence chain #46/B7
Alignment identifier is 46/B7
> sequence chain #46/B8
Alignment identifier is 46/B8
> sequence chain #46/B9
Alignment identifier is 46/B9
> sequence chain #46/CA
Alignment identifier is 46/CA
> sequence chain #46/CB
Alignment identifier is 46/CB
> sequence chain #46/CC
Alignment identifier is 46/CC
> sequence chain #46/CD
Alignment identifier is 46/CD
> sequence chain #46/CE
Alignment identifier is 46/CE
> sequence chain #46/CF
Alignment identifier is 46/CF
> sequence chain #46/CG
Alignment identifier is 46/CG
> sequence chain #46/CH
Alignment identifier is 46/CH
> sequence chain #46/CI
Alignment identifier is 46/CI
> sequence chain #46/CJ
Alignment identifier is 46/CJ
> sequence chain #46/CK
Alignment identifier is 46/CK
> sequence chain #46/CL
Alignment identifier is 46/CL
> sequence chain #46/CM
Alignment identifier is 46/CM
> sequence chain #46/CN
Alignment identifier is 46/CN
> sequence chain #46/CO
Alignment identifier is 46/CO
> sequence chain #46/CP
Alignment identifier is 46/CP
> sequence chain #46/CQ
Alignment identifier is 46/CQ
> sequence chain #46/CR
Alignment identifier is 46/CR
> sequence chain #46/CS
Alignment identifier is 46/CS
> sequence chain #46/CT
Alignment identifier is 46/CT
> sequence chain #46/CU
Alignment identifier is 46/CU
> sequence chain #46/CV#50/DM
Alignment identifier is 33
> sequence chain #46/CX
Alignment identifier is 46/CX
> sequence chain #46/Cb,DA,Ds#50/Cs,Dc
Alignment identifier is 34
> sequence chain #46/Cc
Alignment identifier is 46/Cc
> sequence chain #46/Cd
Alignment identifier is 46/Cd
> sequence chain #46/Cf,Dm
Alignment identifier is 35
> sequence chain #46/Ch
Alignment identifier is 46/Ch
> sequence chain #46/Ci,DQ#50/Ce,Df
Alignment identifier is 36
> sequence chain #46/Cj#50/Db
Alignment identifier is 37
> sequence chain #46/Cm#50/l,Ca,Cc,DV,D7
Alignment identifier is 38
> sequence chain #46/Cn#50/Ax,Ci
Alignment identifier is 39
> sequence chain #46/Co,DB,Dd
Alignment identifier is 40
> sequence chain #46/Cq,Dr#50/t,3
Alignment identifier is 41
> sequence chain #46/Ct,DM#50/Dv
Alignment identifier is 42
> sequence chain #46/Cv,C6,D0#50/Cu
Alignment identifier is 43
> sequence chain #46/Cw
Alignment identifier is 46/Cw
> sequence chain #46/Cy
Alignment identifier is 46/Cy
> sequence chain #46/C3
Alignment identifier is 46/C3
> sequence chain #46/C4
Alignment identifier is 46/C4
> sequence chain #46/C5#50/AB,C7
Alignment identifier is 44
> sequence chain #46/C7
Alignment identifier is 46/C7
> sequence chain #46/DD
Alignment identifier is 46/DD
> sequence chain #46/DG#50/Aj,Ch,Cw
Alignment identifier is 45
> sequence chain #46/DI
Alignment identifier is 46/DI
> sequence chain #46/DJ
Alignment identifier is 46/DJ
> sequence chain #46/DK
Alignment identifier is 46/DK
> sequence chain #46/DO#50/Cd,Di,Dt
Alignment identifier is 46
> sequence chain #46/DR
Alignment identifier is 46/DR
> sequence chain #46/DT#50/Ap
Alignment identifier is 47
> sequence chain #46/DU
Alignment identifier is 46/DU
> sequence chain #46/DV#50/W,p
Alignment identifier is 48
> sequence chain #46/DX,Db#50/DN
Alignment identifier is 49
> sequence chain #46/DY#50/9,D8
Alignment identifier is 50
> sequence chain #46/DZ#50/C9,DX
Alignment identifier is 51
> sequence chain #46/Dc#50/n
Alignment identifier is 52
> sequence chain #46/Di,Dl,Do#50/AI
Alignment identifier is 53
> sequence chain #46/Dn
Alignment identifier is 46/Dn
> sequence chain #46/Du
Alignment identifier is 46/Du
> sequence chain #46/Dx
Alignment identifier is 46/Dx
> sequence chain #46/D1
Alignment identifier is 46/D1
> sequence chain #46/D7
Alignment identifier is 46/D7
> sequence chain #49/Aa
Alignment identifier is 49/Aa
> sequence chain #49/Ab
Alignment identifier is 49/Ab
> sequence chain #49/Ca
Alignment identifier is 49/Ca
> sequence chain #49/Ba
Alignment identifier is 49/Ba
> sequence chain #49/Bb
Alignment identifier is 49/Bb
> sequence chain #49/Ac
Alignment identifier is 49/Ac
> sequence chain #49/Cb
Alignment identifier is 49/Cb
> sequence chain #49/Cc
Alignment identifier is 49/Cc
> sequence chain #49/Bc
Alignment identifier is 49/Bc
> sequence chain #49/Ad
Alignment identifier is 49/Ad
> sequence chain #49/Ae
Alignment identifier is 49/Ae
> sequence chain #50/A
Alignment identifier is 50/A
> sequence chain #50/B
Alignment identifier is 50/B
> sequence chain #50/C
Alignment identifier is 50/C
> sequence chain #50/D
Alignment identifier is 50/D
> sequence chain #50/E
Alignment identifier is 50/E
> sequence chain #50/F
Alignment identifier is 50/F
> sequence chain #50/G
Alignment identifier is 50/G
> sequence chain #50/H
Alignment identifier is 50/H
> sequence chain #50/I
Alignment identifier is 50/I
> sequence chain #50/J
Alignment identifier is 50/J
> sequence chain #50/K
Alignment identifier is 50/K
> sequence chain #50/L
Alignment identifier is 50/L
> sequence chain #50/M
Alignment identifier is 50/M
> sequence chain #50/N
Alignment identifier is 50/N
> sequence chain #50/O
Alignment identifier is 50/O
> sequence chain #50/P
Alignment identifier is 50/P
> sequence chain #50/Q
Alignment identifier is 50/Q
> sequence chain #50/R
Alignment identifier is 50/R
> sequence chain #50/S
Alignment identifier is 50/S
> sequence chain #50/T
Alignment identifier is 50/T
> sequence chain #50/V
Alignment identifier is 50/V
> sequence chain #50/X
Alignment identifier is 50/X
> sequence chain #50/Y
Alignment identifier is 50/Y
> sequence chain #50/Z,DC
Alignment identifier is 54
> sequence chain #50/b
Alignment identifier is 50/b
> sequence chain #50/c
Alignment identifier is 50/c
> sequence chain #50/d
Alignment identifier is 50/d
> sequence chain #50/e
Alignment identifier is 50/e
> sequence chain #50/f
Alignment identifier is 50/f
> sequence chain #50/g
Alignment identifier is 50/g
> sequence chain #50/h
Alignment identifier is 50/h
> sequence chain #50/i
Alignment identifier is 50/i
> sequence chain #50/k
Alignment identifier is 50/k
> sequence chain #50/m
Alignment identifier is 50/m
> sequence chain #50/o
Alignment identifier is 50/o
> sequence chain #50/q
Alignment identifier is 50/q
> sequence chain #50/r,A8
Alignment identifier is 55
> sequence chain #50/w
Alignment identifier is 50/w
> sequence chain #50/x,4
Alignment identifier is 56
> sequence chain #50/z
Alignment identifier is 50/z
> sequence chain #50/1
Alignment identifier is 50/1
> sequence chain #50/2,A7
Alignment identifier is 57
> sequence chain #50/8
Alignment identifier is 50/8
> sequence chain #50/AA
Alignment identifier is 50/AA
> sequence chain #50/AD
Alignment identifier is 50/AD
> sequence chain #50/AE,An,BA
Alignment identifier is 58
> sequence chain #50/AF
Alignment identifier is 50/AF
> sequence chain #50/AG
Alignment identifier is 50/AG
> sequence chain #50/AH
Alignment identifier is 50/AH
> sequence chain #50/AJ
Alignment identifier is 50/AJ
> sequence chain #50/AK,DO
Alignment identifier is 59
> sequence chain #50/AL
Alignment identifier is 50/AL
> sequence chain #50/AM
Alignment identifier is 50/AM
> sequence chain #50/AN
Alignment identifier is 50/AN
> sequence chain #50/AO
Alignment identifier is 50/AO
> sequence chain #50/AP,DD
Alignment identifier is 60
> sequence chain #50/AQ
Alignment identifier is 50/AQ
> sequence chain #50/AS
Alignment identifier is 50/AS
> sequence chain #50/AT
Alignment identifier is 50/AT
> sequence chain #50/AU
Alignment identifier is 50/AU
> sequence chain #50/AV
Alignment identifier is 50/AV
> sequence chain #50/AW
Alignment identifier is 50/AW
> sequence chain #50/AX
Alignment identifier is 50/AX
> sequence chain #50/AY
Alignment identifier is 50/AY
> sequence chain #50/Aa
Alignment identifier is 50/Aa
> sequence chain #50/Ab
Alignment identifier is 50/Ab
> sequence chain #50/Ac
Alignment identifier is 50/Ac
> sequence chain #50/Ad
Alignment identifier is 50/Ad
> sequence chain #50/Ae
Alignment identifier is 50/Ae
> sequence chain #50/Af
Alignment identifier is 50/Af
> sequence chain #50/Ah
Alignment identifier is 50/Ah
> sequence chain #50/Ai
Alignment identifier is 50/Ai
> sequence chain #50/Ak
Alignment identifier is 50/Ak
> sequence chain #50/Am
Alignment identifier is 50/Am
> sequence chain #50/Ao
Alignment identifier is 50/Ao
> sequence chain #50/Aq
Alignment identifier is 50/Aq
> sequence chain #50/Ar
Alignment identifier is 50/Ar
> sequence chain #50/As
Alignment identifier is 50/As
> sequence chain #50/At
Alignment identifier is 50/At
> sequence chain #50/Au,DS
Alignment identifier is 61
> sequence chain #50/Av
Alignment identifier is 50/Av
> sequence chain #50/Aw,Ck
Alignment identifier is 62
> sequence chain #50/Az
Alignment identifier is 50/Az
> sequence chain #50/A0
Alignment identifier is 50/A0
> sequence chain #50/A2
Alignment identifier is 50/A2
> sequence chain #50/A4
Alignment identifier is 50/A4
> sequence chain #50/A5
Alignment identifier is 50/A5
> sequence chain #50/A6
Alignment identifier is 50/A6
> sequence chain #50/A9
Alignment identifier is 50/A9
> sequence chain #50/BB
Alignment identifier is 50/BB
> sequence chain #50/BC
Alignment identifier is 50/BC
> sequence chain #50/BD
Alignment identifier is 50/BD
> sequence chain #50/BE
Alignment identifier is 50/BE
> sequence chain #50/BG
Alignment identifier is 50/BG
> sequence chain #50/BH
Alignment identifier is 50/BH
> sequence chain #50/BI
Alignment identifier is 50/BI
> sequence chain #50/BJ
Alignment identifier is 50/BJ
> sequence chain #50/BK
Alignment identifier is 50/BK
> sequence chain #50/BL
Alignment identifier is 50/BL
> sequence chain #50/BN
Alignment identifier is 50/BN
> sequence chain #50/BO
Alignment identifier is 50/BO
> sequence chain #50/BP
Alignment identifier is 50/BP
> sequence chain #50/BQ
Alignment identifier is 50/BQ
> sequence chain #50/BR
Alignment identifier is 50/BR
> sequence chain #50/BS
Alignment identifier is 50/BS
> sequence chain #50/BT
Alignment identifier is 50/BT
> sequence chain #50/BU
Alignment identifier is 50/BU
> sequence chain #50/BV
Alignment identifier is 50/BV
> sequence chain #50/BW
Alignment identifier is 50/BW
> sequence chain #50/BX
Alignment identifier is 50/BX
> sequence chain #50/BY
Alignment identifier is 50/BY
> sequence chain #50/BZ
Alignment identifier is 50/BZ
> sequence chain #50/Ba
Alignment identifier is 50/Ba
> sequence chain #50/Bb
Alignment identifier is 50/Bb
> sequence chain #50/Bc
Alignment identifier is 50/Bc
> sequence chain #50/Bd
Alignment identifier is 50/Bd
> sequence chain #50/Be
Alignment identifier is 50/Be
> sequence chain #50/Bf
Alignment identifier is 50/Bf
> sequence chain #50/Bg
Alignment identifier is 50/Bg
> sequence chain #50/Bh
Alignment identifier is 50/Bh
> sequence chain #50/Bi
Alignment identifier is 50/Bi
> sequence chain #50/Bj
Alignment identifier is 50/Bj
> sequence chain #50/Bk
Alignment identifier is 50/Bk
> sequence chain #50/Bl
Alignment identifier is 50/Bl
> sequence chain #50/Bm
Alignment identifier is 50/Bm
> sequence chain #50/Bn
Alignment identifier is 50/Bn
> sequence chain #50/Bp
Alignment identifier is 50/Bp
> sequence chain #50/Bq
Alignment identifier is 50/Bq
> sequence chain #50/Br
Alignment identifier is 50/Br
> sequence chain #50/Bs
Alignment identifier is 50/Bs
> sequence chain #50/Bt
Alignment identifier is 50/Bt
> sequence chain #50/Bu
Alignment identifier is 50/Bu
> sequence chain #50/Bv
Alignment identifier is 50/Bv
> sequence chain #50/Bw
Alignment identifier is 50/Bw
> sequence chain #50/Bx
Alignment identifier is 50/Bx
> sequence chain #50/By
Alignment identifier is 50/By
> sequence chain #50/Bz
Alignment identifier is 50/Bz
> sequence chain #50/B0
Alignment identifier is 50/B0
> sequence chain #50/B1
Alignment identifier is 50/B1
> sequence chain #50/B2
Alignment identifier is 50/B2
> sequence chain #50/B3
Alignment identifier is 50/B3
> sequence chain #50/B4
Alignment identifier is 50/B4
> sequence chain #50/B5
Alignment identifier is 50/B5
> sequence chain #50/B6
Alignment identifier is 50/B6
> sequence chain #50/B7
Alignment identifier is 50/B7
> sequence chain #50/B8
Alignment identifier is 50/B8
> sequence chain #50/B9
Alignment identifier is 50/B9
> sequence chain #50/CA
Alignment identifier is 50/CA
> sequence chain #50/CB
Alignment identifier is 50/CB
> sequence chain #50/CC
Alignment identifier is 50/CC
> sequence chain #50/CD
Alignment identifier is 50/CD
> sequence chain #50/CE
Alignment identifier is 50/CE
> sequence chain #50/CF
Alignment identifier is 50/CF
> sequence chain #50/CG
Alignment identifier is 50/CG
> sequence chain #50/CH
Alignment identifier is 50/CH
> sequence chain #50/CI
Alignment identifier is 50/CI
> sequence chain #50/CJ
Alignment identifier is 50/CJ
> sequence chain #50/CK
Alignment identifier is 50/CK
> sequence chain #50/CL
Alignment identifier is 50/CL
> sequence chain #50/CM
Alignment identifier is 50/CM
> sequence chain #50/CN
Alignment identifier is 50/CN
> sequence chain #50/CO
Alignment identifier is 50/CO
> sequence chain #50/CP
Alignment identifier is 50/CP
> sequence chain #50/CQ
Alignment identifier is 50/CQ
> sequence chain #50/CR
Alignment identifier is 50/CR
> sequence chain #50/CS
Alignment identifier is 50/CS
> sequence chain #50/CT
Alignment identifier is 50/CT
> sequence chain #50/CU
Alignment identifier is 50/CU
> sequence chain #50/CV
Alignment identifier is 50/CV
> sequence chain #50/CW
Alignment identifier is 50/CW
> sequence chain #50/CX
Alignment identifier is 50/CX
> sequence chain #50/CY
Alignment identifier is 50/CY
> sequence chain #50/Cb
Alignment identifier is 50/Cb
> sequence chain #50/Cg
Alignment identifier is 50/Cg
> sequence chain #50/Cz,DI
Alignment identifier is 63
> sequence chain #50/C6,D0,D5
Alignment identifier is 64
> sequence chain #50/C8
Alignment identifier is 50/C8
> sequence chain #50/DB,D2
Alignment identifier is 65
> sequence chain #50/DG
Alignment identifier is 50/DG
> sequence chain #50/De
Alignment identifier is 50/De
> sequence chain #50/Dg
Alignment identifier is 50/Dg
> sequence chain #50/Dj
Alignment identifier is 50/Dj
> sequence chain #50/Dn
Alignment identifier is 50/Dn
> sequence chain #50/Dp
Alignment identifier is 50/Dp
> sequence chain #50/Dy
Alignment identifier is 50/Dy
> sequence chain #50/D6
Alignment identifier is 50/D6
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/amy/Desktop/SPA
> AAT_HNE/3C11_Fab_AAT_NE/3c11_aat_hen_csparc.cxs"
Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300,
pixel 0.867, shown at level 0.0665, step 2, values float32
Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at
level 0.0841, step 1, values float32
Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size
300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32
Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size
180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32
Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867,
shown at level 0.0503, step 2, values float32
Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel
0.867, shown at level 0.0806, step 1, values float32
Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size
128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32
Opened cryosparc_P371_J937_003_volume_map.mrc as #14, grid size 300,300,300,
pixel 0.867, shown at level 0.0245, step 2, values float32
Opened cryosparc_P371_J937_003_volume_map.mrc z flip as #15, grid size
300,300,300, pixel 0.867, shown at level 0.0683, step 1, values float32
Opened cryosparc_P371_J948_003_volume_map.mrc as #21, grid size 300,300,300,
pixel 0.867, shown at level 0.0208, step 2, values float32
Opened cryosparc_P371_J948_003_volume_map.mrc z flip as #22, grid size
300,300,300, pixel 0.867, shown at level 0.0938, step 1, values float32
Opened J1122.mrc as #29, grid size 300,300,300, pixel 0.867, shown at level
0.071, step 2, values float32
Opened J1134.mrc as #34, grid size 300,300,300, pixel 0.867, shown at level
0.0707, step 2, values float32
Opened cryosparc_P483_molmap_of_combined_6A.mrc as #41, grid size 200,200,200,
pixel 1, shown at level 0.293, step 1, values float32
Opened AATHNEcombined map 6 as #8, grid size 43,51,63, pixel 2, shown at level
0.366, step 1, values float32
Opened copy of copy of AATHNEcombined map 6 as #45, grid size 43,51,63, pixel
2, shown at level 0.354, step 1, values float32
Log from Thu Mar 12 17:49:41 2026UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/amy/Desktop/SPA AAT_HNE/csparc.cxs"
Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300,
pixel 0.867, shown at level 0.0665, step 2, values float32
Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at
level 0.0841, step 1, values float32
Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size
300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32
Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size
180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32
Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867,
shown at level 0.0503, step 2, values float32
Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel
0.867, shown at level 0.0806, step 1, values float32
Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size
128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32
Opened cryosparc_P371_J937_003_volume_map.mrc as #14, grid size 300,300,300,
pixel 0.867, shown at level 0.0245, step 2, values float32
Opened cryosparc_P371_J937_003_volume_map.mrc z flip as #15, grid size
300,300,300, pixel 0.867, shown at level 0.0683, step 1, values float32
Opened cryosparc_P371_J948_003_volume_map.mrc as #21, grid size 300,300,300,
pixel 0.867, shown at level 0.0208, step 2, values float32
Opened cryosparc_P371_J948_003_volume_map.mrc z flip as #22, grid size
300,300,300, pixel 0.867, shown at level 0.0938, step 1, values float32
Opened J1122.mrc as #29, grid size 300,300,300, pixel 0.867, shown at level
0.071, step 2, values float32
Opened J1134.mrc as #34, grid size 300,300,300, pixel 0.867, shown at level
0.0707, step 2, values float32
Log from Wed Feb 11 13:24:40 2026UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/amy/Desktop/3C11_Fab_AAT_NE/csparc.cxs
Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300,
pixel 0.867, shown at level 0.0665, step 2, values float32
Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at
level 0.0841, step 1, values float32
Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size
300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32
Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size
180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32
Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867,
shown at level 0.0503, step 2, values float32
Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel
0.867, shown at level 0.0806, step 1, values float32
Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size
128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32
Opened cryosparc_P371_J937_003_volume_map.mrc as #14, grid size 300,300,300,
pixel 0.867, shown at level 0.0245, step 2, values float32
Opened cryosparc_P371_J937_003_volume_map.mrc z flip as #15, grid size
300,300,300, pixel 0.867, shown at level 0.0683, step 1, values float32
Opened cryosparc_P371_J948_003_volume_map.mrc as #21, grid size 300,300,300,
pixel 0.867, shown at level 0.0208, step 2, values float32
Opened cryosparc_P371_J948_003_volume_map.mrc z flip as #22, grid size
300,300,300, pixel 0.867, shown at level 0.0938, step 1, values float32
Opened J1122.mrc as #29, grid size 300,300,300, pixel 0.867, shown at level
0.071, step 2, values float32
Opened J1134.mrc as #34, grid size 300,300,300, pixel 0.867, shown at level
0.0707, step 2, values float32
Log from Sun Feb 1 23:24:08 2026UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/amy/Desktop/3C11_Fab_AAT_NE/csparc.cxs format session
Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300,
pixel 0.867, shown at level 0.0665, step 2, values float32
Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at
level 0.0841, step 1, values float32
Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size
300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32
Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size
180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32
Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867,
shown at level 0.0503, step 2, values float32
Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel
0.867, shown at level 0.0806, step 1, values float32
Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size
128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32
Opened cryosparc_P371_J937_003_volume_map.mrc as #14, grid size 300,300,300,
pixel 0.867, shown at level 0.0245, step 2, values float32
Opened cryosparc_P371_J937_003_volume_map.mrc z flip as #15, grid size
300,300,300, pixel 0.867, shown at level 0.0683, step 1, values float32
Opened cryosparc_P371_J948_003_volume_map.mrc as #21, grid size 300,300,300,
pixel 0.867, shown at level 0.0208, step 2, values float32
Opened cryosparc_P371_J948_003_volume_map.mrc z flip as #22, grid size
300,300,300, pixel 0.867, shown at level 0.0938, step 1, values float32
Opened J1122.mrc as #29, grid size 300,300,300, pixel 0.867, shown at level
0.071, step 2, values float32
Opened J1134.mrc as #34, grid size 300,300,300, pixel 0.867, shown at level
0.0707, step 2, values float32
Log from Tue Jan 6 13:31:49 2026UCSF ChimeraX version: 1.9rc202411230619
(2024-11-23)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/apple/Downloads/csparc.cxs
Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300,
pixel 0.867, shown at level 0.0665, step 2, values float32
Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at
level 0.0841, step 1, values float32
Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size
300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32
Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size
180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32
Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867,
shown at level 0.0503, step 2, values float32
Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel
0.867, shown at level 0.0806, step 1, values float32
Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size
128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32
Opened cryosparc_P371_J937_003_volume_map.mrc as #14, grid size 300,300,300,
pixel 0.867, shown at level 0.0245, step 2, values float32
Opened cryosparc_P371_J937_003_volume_map.mrc z flip as #15, grid size
300,300,300, pixel 0.867, shown at level 0.0683, step 1, values float32
Opened cryosparc_P371_J948_003_volume_map.mrc as #21, grid size 300,300,300,
pixel 0.867, shown at level 0.0208, step 2, values float32
Opened cryosparc_P371_J948_003_volume_map.mrc z flip as #22, grid size
300,300,300, pixel 0.867, shown at level 0.0938, step 1, values float32
Log from Wed Dec 31 02:28:23 2025UCSF ChimeraX version: 1.9rc202411230619
(2024-11-23)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/apple/Downloads/csparc.cxs
Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300,
pixel 0.867, shown at level 0.0665, step 2, values float32
Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at
level 0.0841, step 1, values float32
Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size
300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32
Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size
180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32
Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867,
shown at level 0.0503, step 2, values float32
Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel
0.867, shown at level 0.0806, step 1, values float32
Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size
128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32
Opened cryosparc_P371_J937_003_volume_map.mrc as #14, grid size 300,300,300,
pixel 0.867, shown at level 0.0245, step 2, values float32
Opened cryosparc_P371_J937_003_volume_map.mrc z flip as #15, grid size
300,300,300, pixel 0.867, shown at level 0.0683, step 1, values float32
Opened cryosparc_P371_J948_003_volume_map.mrc as #21, grid size 300,300,300,
pixel 0.867, shown at level 0.0208, step 2, values float32
Opened cryosparc_P371_J948_003_volume_map.mrc z flip as #22, grid size
300,300,300, pixel 0.867, shown at level 0.0938, step 1, values float32
Log from Wed Dec 10 00:50:43 2025UCSF ChimeraX version: 1.9rc202411230619
(2024-11-23)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/apple/Downloads/csparc.cxs
Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300,
pixel 0.867, shown at level 0.0665, step 2, values float32
Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at
level 0.0841, step 1, values float32
Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size
300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32
Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size
180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32
Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867,
shown at level 0.0503, step 2, values float32
Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel
0.867, shown at level 0.0806, step 1, values float32
Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size
128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32
Log from Fri Nov 28 18:17:17 2025UCSF ChimeraX version: 1.9rc202411230619
(2024-11-23)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/apple/Downloads/csparc.cxs
Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300,
pixel 0.867, shown at level 0.0665, step 2, values float32
Opened flipped_J880.mrc as #3, grid size 300,300,300, pixel 0.867, shown at
level 0.0841, step 1, values float32
Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size
300,300,300, pixel 0.867, shown at level 0.0602, step 1, values float32
Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size
180,180,180, pixel 1.44, shown at level 0.122, step 1, values float32
Log from Tue Nov 25 15:20:48 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9rc202411230619 (2024-11-23)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 1ezx format mmcif fromDatabase pdb
1ezx title:
Crystal structure of A serpin:protease complex [more info...]
Chain information for 1ezx #1
---
Chain | Description | UniProt
A | ALPHA-1-ANTITRYPSIN | A1AT_HUMAN 24-358
B | ALPHA-1-ANTITRYPSIN | A1AT_HUMAN 359-394
C | TRYPSIN | TRY1_BOVIN 42-245
> open /Users/apple/Downloads/cryosparc_P371_J880_003_volume_map.mrc
Opened cryosparc_P371_J880_003_volume_map.mrc as #2, grid size 300,300,300,
pixel 0.867, shown at level 0.0177, step 2, values float32
> volume #2 level 0.06652
> ui mousemode right "translate selected models"
> select add #1
3984 atoms, 3982 bonds, 5 pseudobonds, 592 residues, 3 models selected
> view matrix models #1,1,0,0,22.115,0,1,0,63.09,0,0,1,71.823
> view matrix models #1,1,0,0,69.177,0,1,0,79.741,0,0,1,64.119
> view matrix models #1,1,0,0,67.012,0,1,0,77.327,0,0,1,54.335
> view matrix models #1,1,0,0,68.613,0,1,0,71.318,0,0,1,51.449
> ui tool show "Fit in Map"
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 3984 atoms
average map value = 0.0438, steps = 92
shifted from previous position = 3.55
rotated from previous position = 4.42 degrees
atoms outside contour = 2880, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.99872483 -0.00989522 0.04950557 63.11308004
0.00699761 0.99827076 0.05836545 67.58136236
-0.04999751 -0.05794461 0.99706703 56.37622316
Axis -0.75528783 0.64614759 0.10969770
Axis point 0.00000000 1024.64866555 -1103.37084637
Rotation angle (degrees) 4.41598404
Shift along axis 2.18333524
> view matrix models
> #1,0.99872,-0.0098952,0.049506,62.468,0.0069976,0.99827,0.058365,78.039,-0.049998,-0.057945,0.99707,58.786
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.95028,-0.27274,-0.15028,221.56,0.30912,-0.88449,-0.34946,175.7,-0.037612,-0.37854,0.92482,78.268
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 3984 atoms
average map value = 0.04798, steps = 140
shifted from previous position = 7.9
rotated from previous position = 12.7 degrees
atoms outside contour = 2817, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
-0.90965137 -0.21420693 -0.35587888 224.37202412
0.34819532 -0.86039384 -0.37213231 169.35532345
-0.22648268 -0.46242602 0.85724429 105.26930309
Axis -0.15458157 -0.22152447 0.96282472
Axis point 107.00674340 114.53127832 0.00000000
Rotation angle (degrees) 163.01876555
Shift along axis 29.15575838
> view matrix models
> #1,-0.93537,-0.33888,0.10125,206.37,0.28885,-0.89713,-0.33425,173.15,0.2041,-0.2834,0.93703,61.97
> remove /C
Unknown command: remove /C
> delete /C
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 2975 atoms
average map value = 0.05683, steps = 168
shifted from previous position = 10.2
rotated from previous position = 20.9 degrees
atoms outside contour = 1876, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
-0.98775248 -0.03216686 0.15267718 185.97005837
0.01404291 -0.99287467 -0.11833294 193.09005228
0.15539570 -0.11473962 0.98116614 52.60294093
Axis 0.07739391 -0.05855237 0.99527976
Axis point 89.79478279 99.15188295 0.00000000
Rotation angle (degrees) 178.66978984
Shift along axis 55.44171271
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 2975 atoms
average map value = 0.05683, steps = 44
shifted from previous position = 0.00306
rotated from previous position = 0.00868 degrees
atoms outside contour = 1876, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
-0.98775300 -0.03230499 0.15264466 185.98147456
0.01419042 -0.99287622 -0.11830233 193.08167122
0.15537901 -0.11468739 0.98117489 52.59959002
Axis 0.07738151 -0.05853153 0.99528195
Axis point 89.79393478 99.15365724 0.00000000
Rotation angle (degrees) 178.66156873
Shift along axis 55.44158488
> view matrix models
> #1,-0.34306,0.064653,-0.93709,202.25,-0.15112,-0.98843,-0.012871,197.23,-0.92708,0.1372,0.34886,143.06
> view matrix models
> #1,0.89084,0.24868,-0.38022,79.922,0.1402,-0.94652,-0.29059,192.22,-0.43215,0.20556,-0.87806,178.59
> view matrix models
> #1,0.98069,0.15076,0.12459,50.828,0.17789,-0.95233,-0.24786,187.69,0.081282,0.26523,-0.96075,146.99
> transparency #2 50
> view matrix models
> #1,0.29239,0.037619,0.95556,53.368,0.22932,-0.97283,-0.03187,173.11,0.9284,0.22844,-0.29308,56.382
> view matrix models
> #1,-0.29179,0.14333,0.94568,84.773,0.13863,-0.97193,0.19008,165.94,0.94638,0.18656,0.26373,25.435
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 2975 atoms
average map value = 0.05731, steps = 92
shifted from previous position = 3.83
rotated from previous position = 8.94 degrees
atoms outside contour = 1851, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
-0.32142151 0.28922900 0.90168442 78.62508488
0.10483022 -0.93549119 0.33744164 157.26649378
0.94111574 0.20298478 0.27036706 21.13366302
Axis -0.58056816 -0.17025957 -0.79621121
Axis point 36.79057462 75.39561878 -0.00000000
Rotation angle (degrees) 173.35036530
Shift along axis -89.25020548
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 2975 atoms
average map value = 0.05731, steps = 76
shifted from previous position = 0.0143
rotated from previous position = 0.0108 degrees
atoms outside contour = 1850, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
-0.32139468 0.28930309 0.90167022 78.61286146
0.10496741 -0.93543603 0.33755190 157.24594170
0.94110961 0.20313337 0.27027676 21.11828838
Axis -0.58058094 -0.17034675 -0.79618324
Axis point 36.78722862 75.38632197 0.00000000
Rotation angle (degrees) 173.35241654
Shift along axis -89.24149146
> view matrix models
> #1,0.48423,0.47971,0.73171,25.463,0.23276,-0.87679,0.42079,140.68,0.84341,-0.033442,-0.53622,88.647
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 2975 atoms
average map value = 0.05854, steps = 96
shifted from previous position = 2.57
rotated from previous position = 9.29 degrees
atoms outside contour = 1796, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.39156198 0.46621567 0.79329828 28.63896931
0.32834063 -0.87617582 0.35285743 137.96501568
0.85957643 0.12230650 -0.49615469 78.33453532
Axis -0.83325343 -0.23954143 -0.49830575
Axis point 0.00000000 66.13906102 25.80824474
Rotation angle (degrees) 172.04797842
Shift along axis -95.94640636
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 2975 atoms
average map value = 0.05854, steps = 72
shifted from previous position = 0.00208
rotated from previous position = 0.0113 degrees
atoms outside contour = 1796, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.39171342 0.46612484 0.79327690 28.63726861
0.32836586 -0.87622221 0.35271873 137.97292978
0.85949779 0.12232039 -0.49628748 78.34647546
Axis -0.83330036 -0.23950649 -0.49824406
Axis point 0.00000000 66.14388335 25.81952433
Rotation angle (degrees) 172.05372561
Shift along axis -95.94452502
> view matrix models
> #1,0.76487,0.62103,0.17117,31.524,0.60943,-0.78369,0.12011,127.91,0.20873,0.012451,-0.97789,154.56
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 2975 atoms
average map value = 0.05756, steps = 152
shifted from previous position = 4.36
rotated from previous position = 22.9 degrees
atoms outside contour = 1854, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.91851505 0.27415782 0.28489928 35.47934780
0.28051968 -0.95965858 0.01908170 161.02943922
0.27863743 0.06239303 -0.95836751 146.25557472
Axis 0.97941439 0.14160128 0.14386290
Axis point 0.00000000 77.18823065 71.36819300
Rotation angle (degrees) 178.73303939
Shift along axis 78.59170916
> view matrix models
> #1,0.70928,0.23412,0.66491,29.192,0.22662,-0.9689,0.099416,160.36,0.6675,0.080168,-0.74028,107.68
> view matrix models
> #1,0.38932,0.16756,0.90573,39.677,0.11688,-0.98435,0.13187,166.42,0.91366,0.054523,-0.40281,73.929
> view matrix models
> #1,0.33533,0.23749,0.91168,38.512,0.22246,-0.9603,0.16833,156.1,0.91546,0.14637,-0.37485,66.587
> view matrix models
> #1,0.33533,0.23749,0.91168,38.861,0.22246,-0.9603,0.16833,151.64,0.91546,0.14637,-0.37485,67.054
> view matrix models
> #1,0.34573,0.097318,0.93327,45.492,0.021529,-0.99517,0.095797,170.8,0.93809,-0.013027,-0.34615,73.665
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 2975 atoms
average map value = 0.05854, steps = 136
shifted from previous position = 9.44
rotated from previous position = 25.1 degrees
atoms outside contour = 1797, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.39128073 0.46623746 0.79342424 28.64047706
0.32828593 -0.87615611 0.35295725 137.95838588
0.85972538 0.12236464 -0.49588220 78.32133865
Axis -0.83316813 -0.23955669 -0.49844103
Axis point 0.00000000 66.13417831 25.79650241
Rotation angle (degrees) 172.04571172
Shift along axis -95.94975542
> view matrix models
> #1,0.39128,0.46624,0.79342,25.073,0.32829,-0.87616,0.35296,137.6,0.85973,0.12236,-0.49588,78.077
> view matrix models
> #1,-0.056102,0.1979,0.97862,59.23,0.073542,-0.97668,0.20173,168.77,0.99571,0.083287,0.04024,40.63
> view matrix models
> #1,-0.064697,0.19676,0.97831,59.866,-0.033318,-0.98025,0.19495,176.2,0.99735,-0.019983,0.069975,45.097
> view matrix models
> #1,-0.064697,0.19676,0.97831,60.856,-0.033318,-0.98025,0.19495,173.38,0.99735,-0.019983,0.069975,44.14
> view matrix models
> #1,-0.064697,0.19676,0.97831,62.425,-0.033318,-0.98025,0.19495,171.85,0.99735,-0.019983,0.069975,46.927
> view matrix models
> #1,0.048374,0.23427,0.97097,53.348,-0.027021,-0.97144,0.23574,168.54,0.99846,-0.037639,-0.040662,54.362
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 2975 atoms
average map value = 0.05548, steps = 116
shifted from previous position = 2.18
rotated from previous position = 10.2 degrees
atoms outside contour = 1897, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.15476290 0.36480201 0.91813285 40.06056626
0.00453943 -0.92958252 0.36858613 155.48377322
0.98794121 -0.05287566 -0.14552088 61.55028255
Axis -0.75418435 -0.12491849 -0.64467149
Axis point 0.00000000 74.79947560 0.01397902
Rotation angle (degrees) 163.77466905
Shift along axis -89.31556288
> view matrix models
> #1,0.15476,0.3648,0.91813,43.614,0.0045394,-0.92958,0.36859,155.22,0.98794,-0.052876,-0.14552,59.521
> view matrix models
> #1,-0.2078,0.33394,0.9194,68.56,-0.052237,-0.94237,0.33048,161.84,0.97677,0.020648,0.21327,34.9
> view matrix models
> #1,-0.21574,0.16972,0.96159,76.632,-0.13117,-0.98089,0.1437,180.08,0.9676,-0.095125,0.23388,41.35
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 2975 atoms
average map value = 0.05783, steps = 140
shifted from previous position = 8.76
rotated from previous position = 14.8 degrees
atoms outside contour = 1859, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
-0.45352763 0.10818223 0.88465208 99.24914335
-0.11633057 -0.99129935 0.06158562 193.39501529
0.88361750 -0.07498130 0.46216655 30.32738546
Axis -0.51968455 0.00393692 -0.85434915
Axis point 47.88058461 94.47454852 0.00000000
Rotation angle (degrees) 172.44984306
Shift along axis -76.72704192
> view matrix models
> #1,-0.44996,0.138,0.88232,97.338,-0.1451,-0.98616,0.080249,193.83,0.88118,-0.091912,0.46376,31.423
> view matrix models
> #1,-0.44996,0.138,0.88232,96.943,-0.1451,-0.98616,0.080249,180.07,0.88118,-0.091912,0.46376,31.456
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 2975 atoms
average map value = 0.05816, steps = 144
shifted from previous position = 5.29
rotated from previous position = 25.5 degrees
atoms outside contour = 1860, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
-0.76791109 0.07342342 0.63633447 137.05037337
0.02287887 -0.98963117 0.14179815 171.02871657
0.64014773 0.12344698 0.75826890 16.52925526
Axis -0.34041716 -0.07073658 -0.93760999
Axis point 66.71618726 84.08739228 0.00000000
Rotation angle (degrees) 178.45546636
Shift along axis -74.25028018
> volume flip #2 axis z
Opened cryosparc_P371_J880_003_volume_map.mrc z flip as #3, grid size
300,300,300, pixel 0.867, shown at step 1, values float32
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 2975 atoms
average map value = 0.05816, steps = 44
shifted from previous position = 0.00304
rotated from previous position = 0.0131 degrees
atoms outside contour = 1859, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
-0.76779231 0.07330789 0.63649111 137.03880955
0.02299050 -0.98964048 0.14171507 171.02535003
0.64028619 0.12344099 0.75815296 16.52599590
Axis -0.34050650 -0.07071503 -0.93757917
Axis point 66.70481841 84.08969330 0.00000000
Rotation angle (degrees) 178.46235923
Shift along axis -74.25109879
> view matrix models
> #1,-0.52389,0.12388,0.84273,106.41,0.091727,-0.97541,0.20041,162.36,0.84683,0.18229,0.49964,14.777
> select add #3
2975 atoms, 2968 bonds, 437 residues, 3 models selected
> select subtract #3
2975 atoms, 2968 bonds, 437 residues, 1 model selected
> view matrix models
> #1,-0.52389,0.12388,0.84273,105.24,0.091727,-0.97541,0.20041,169.49,0.84683,0.18229,0.49964,54.589
> view matrix models
> #1,-0.52389,0.12388,0.84273,103,0.091727,-0.97541,0.20041,168.04,0.84683,0.18229,0.49964,53.744
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 2975 atoms
average map value = 0.05198, steps = 396
shifted from previous position = 26.6
rotated from previous position = 41.8 degrees
atoms outside contour = 2024, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
-0.40282969 0.31103532 0.86080501 84.94134983
0.59685966 -0.62373813 0.50468732 103.56065454
0.69389249 0.71708282 0.06561581 32.32204409
Axis 0.54006522 0.42441412 0.72677522
Axis point 26.67261820 43.96459459 0.00000000
Rotation angle (degrees) 168.65952926
Shift along axis 113.31733317
> view matrix models
> #1,-0.43926,0.065153,0.89599,100.22,0.59516,-0.72598,0.34457,119.21,0.67293,0.68462,0.28012,23.176
> view matrix models
> #1,-0.43926,0.065153,0.89599,90.909,0.59516,-0.72598,0.34457,101.79,0.67293,0.68462,0.28012,39.972
> view matrix models
> #1,-0.86466,-0.41381,0.28483,182.78,0.49939,-0.76955,0.39798,107.46,0.054503,0.48636,0.87206,57.135
> view matrix models
> #1,-0.41714,-0.50359,-0.75657,220.21,0.34751,-0.85757,0.37922,123.61,-0.83978,-0.10473,0.53273,169.98
> view matrix models
> #1,0.75417,0.076431,-0.65222,104.02,0.19721,-0.97372,0.11393,155.7,-0.62637,-0.21455,-0.74942,237.56
> view matrix models
> #1,0.59893,0.091914,-0.79551,121.31,0.19286,-0.98071,0.031893,161.17,-0.77723,-0.17253,-0.6051,236.24
> view matrix models
> #1,0.59893,0.091914,-0.79551,120.05,0.19286,-0.98071,0.031893,163.86,-0.77723,-0.17253,-0.6051,238.3
> view matrix models
> #1,0.60587,0.10394,-0.78874,118.48,0.22025,-0.97459,0.040753,161.22,-0.76446,-0.19841,-0.61337,239.55
> view matrix models
> #1,0.60587,0.10394,-0.78874,137.03,0.22025,-0.97459,0.040753,164.86,-0.76446,-0.19841,-0.61337,244.11
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 2975 atoms
average map value = 0.05241, steps = 240
shifted from previous position = 27.2
rotated from previous position = 10.6 degrees
atoms outside contour = 2020, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.57403834 -0.00393553 -0.81881897 142.71357757
0.04701479 -0.99818033 0.03775763 187.83819388
-0.81747758 -0.06017093 -0.57280875 212.09998405
Axis -0.88704943 -0.01215043 0.46151455
Axis point 0.00000000 96.46648529 140.25698861
Rotation angle (degrees) 176.83571969
Shift along axis -30.98908429
> view matrix models
> #1,0.50366,0.028512,-0.86343,147.82,0.16923,-0.98335,0.066244,177.48,-0.84716,-0.17948,-0.5001,217.05
> view matrix models
> #1,0.50366,0.028512,-0.86343,159.38,0.16923,-0.98335,0.066244,163.53,-0.84716,-0.17948,-0.5001,218.36
> view matrix models
> #1,0.77888,-0.021397,-0.6268,131.11,0.011385,-0.99877,0.048242,175.59,-0.62706,-0.044711,-0.77768,212.22
> view matrix models
> #1,0.80541,-0.036391,-0.5916,128.29,-0.023432,-0.99929,0.029569,178.93,-0.59225,-0.0099531,-0.80569,209.51
> view matrix models
> #1,0.80541,-0.036391,-0.5916,124.59,-0.023432,-0.99929,0.029569,182.08,-0.59225,-0.0099531,-0.80569,208.91
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 2975 atoms
average map value = 0.06114, steps = 180
shifted from previous position = 15
rotated from previous position = 14.2 degrees
atoms outside contour = 1746, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.85347860 0.03851228 -0.51970287 104.90951223
-0.07623353 -0.97731057 -0.19761705 201.13931543
-0.51552180 0.20828070 -0.83117774 180.17182734
Axis 0.96224006 -0.00991186 -0.27202175
Axis point 0.00000000 90.37179533 116.08940430
Rotation angle (degrees) 167.82414204
Shift along axis 49.94381521
> view matrix models
> #1,0.85348,0.038512,-0.5197,94.645,-0.076234,-0.97731,-0.19762,192.73,-0.51552,0.20828,-0.83118,215.52
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 2975 atoms
average map value = 0.04998, steps = 228
shifted from previous position = 24.7
rotated from previous position = 22.8 degrees
atoms outside contour = 2007, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.83373907 0.05761081 -0.54914494 106.68752994
-0.27258804 -0.82195371 -0.50008786 229.20333513
-0.48018219 0.56663312 -0.66959090 165.21182517
Axis 0.95346344 -0.06164073 -0.29514047
Axis point 0.00000000 89.71271679 136.26536856
Rotation angle (degrees) 145.98619039
Shift along axis 38.83370161
> view matrix models
> #1,0.85957,-0.051768,-0.50839,109.34,-0.30914,-0.84485,-0.43665,229.25,-0.40691,0.5325,-0.74221,166.84
> view matrix models
> #1,0.85957,-0.051768,-0.50839,105.72,-0.30914,-0.84485,-0.43665,214.62,-0.40691,0.5325,-0.74221,185.48
> view matrix models
> #1,0.90687,0.19702,-0.37252,79.626,0.12723,-0.97073,-0.20369,180.91,-0.40175,0.13732,-0.90539,218.74
> view matrix models
> #1,0.67914,0.18357,0.71068,32.037,0.24568,-0.96923,0.015585,160.52,0.69167,0.16401,-0.70334,135.59
> view matrix models
> #1,0.17493,0.05579,0.983,56.185,0.11322,-0.99291,0.036205,169.22,0.97805,0.10496,-0.18,90.508
> view matrix models
> #1,0.77968,0.065182,0.62277,37.951,0.11391,-0.99274,-0.038712,173.52,0.61572,0.10113,-0.78145,148.81
> view matrix models
> #1,0.92537,0.30742,-0.22176,62.951,0.27327,-0.94648,-0.17175,168.25,-0.26269,0.09833,-0.95986,215.41
> view matrix models
> #1,0.70434,0.40439,-0.58342,92.157,0.29038,-0.9141,-0.28304,171.65,-0.64776,0.02994,-0.76126,232.61
> view matrix models
> #1,0.63232,0.36591,-0.68285,104.88,0.25844,-0.93057,-0.25933,173.32,-0.73033,-0.012492,-0.68298,235.92
> view matrix models
> #1,0.63232,0.36591,-0.68285,105.28,0.25844,-0.93057,-0.25933,173.87,-0.73033,-0.012492,-0.68298,234.43
> view matrix models
> #1,0.62644,0.35038,-0.69628,107.38,0.25038,-0.93639,-0.24594,173.97,-0.73816,-0.020267,-0.67432,234.9
> fitmap #1 inMap #2
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc (#2)
using 2975 atoms
average map value = 0.04135, steps = 172
shifted from previous position = 17.5
rotated from previous position = 15.7 degrees
atoms outside contour = 2209, contour level = 0.066523
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.64106806 0.54805599 -0.53727682 84.29416786
0.45670740 -0.83502441 -0.30684294 171.83349628
-0.61680637 -0.04867109 -0.78560870 224.33733641
Axis 0.90532451 0.27888420 -0.32032972
Axis point 0.00000000 63.39099370 133.30398496
Rotation angle (degrees) 171.80252826
Shift along axis 52.37330856
> volume #3 level 0.08411
> view matrix models
> #1,0.89403,0.11377,0.43333,38.242,0.12475,-0.99218,0.0031177,184.59,0.43029,0.051272,-0.90123,158.14
> view matrix models
> #1,-0.18632,0.03739,0.98178,79.976,-0.079477,-0.99657,0.02287,196.75,0.97927,-0.073767,0.18865,67.401
> view matrix models
> #1,-0.90953,0.27518,-0.3115,186.77,-0.18965,-0.94164,-0.2781,217.91,-0.36985,-0.19387,0.90864,118.99
> view matrix models
> #1,0.24398,0.16972,-0.95481,156.97,0.38319,-0.92132,-0.065848,167.79,-0.89086,-0.34981,-0.28982,231.39
> view matrix models
> #1,0.42166,0.25626,-0.86979,135.42,0.41641,-0.90683,-0.065311,164.75,-0.80549,-0.33465,-0.48908,236.59
> view matrix models
> #1,0.47933,0.24843,-0.84174,130.58,0.4184,-0.90778,-0.029658,162.61,-0.77148,-0.33797,-0.53907,237.53
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.47933,0.24843,-0.84174,128.8,0.4184,-0.90778,-0.029658,153.85,-0.77148,-0.33797,-0.53907,247.51
> fitmap #1 inMap #3
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc z flip
(#3) using 2975 atoms
average map value = 0.05446, steps = 68
shifted from previous position = 3.18
rotated from previous position = 7.84 degrees
atoms outside contour = 2178, contour level = 0.08411
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc z
flip (#3) coordinates:
Matrix rotation and translation
0.52841759 0.14565472 -0.83639676 133.99651702
0.41790523 -0.90217777 0.10691341 147.19357847
-0.73900613 -0.40602951 -0.53759648 249.57659595
Axis -0.87112860 -0.16539807 0.46236180
Axis point 0.00000000 83.46704951 147.99690601
Rotation angle (degrees) 162.87766715
Shift along axis -25.67904816
> view matrix models
> #1,0.228,0.04128,-0.97279,167.46,0.36006,-0.93185,0.04485,156.3,-0.90464,-0.36049,-0.22733,239.34
> view matrix models
> #1,0.228,0.04128,-0.97279,168.72,0.36006,-0.93185,0.04485,153.1,-0.90464,-0.36049,-0.22733,238.66
> fitmap #1 inMap #3
Fit molecule 1ezx (#1) to map cryosparc_P371_J880_003_volume_map.mrc z flip
(#3) using 2975 atoms
average map value = 0.08066, steps = 176
shifted from previous position = 5.39
rotated from previous position = 39.4 degrees
atoms outside contour = 1661, contour level = 0.08411
Position of 1ezx (#1) relative to cryosparc_P371_J880_003_volume_map.mrc z
flip (#3) coordinates:
Matrix rotation and translation
-0.38244590 0.10991711 -0.91741668 203.00581119
0.07750617 -0.98558322 -0.15039445 183.86146589
-0.92072141 -0.12862319 0.36841301 193.39522834
Axis 0.55561740 0.08433916 -0.82714945
Axis point 167.56182272 100.48395710 0.00000000
Rotation angle (degrees) 178.87739199
Shift along axis -31.66647401
> save /Users/apple/Downloads/csparc.cxs includeMaps true
> select subtract #1
Nothing selected
> select add #3
2 models selected
> save /Users/apple/Downloads/flipped_J880.mrc models #3
> open /Users/apple/Downloads/3C11_Fab_D_1292144377_model-annotate_P1_HL-
> coot-0.pdb /Users/apple/Downloads/1ezx_moved-coot-0.pdb
Summary of feedback from opening
/Users/apple/Downloads/3C11_Fab_D_1292144377_model-annotate_P1_HL-coot-0.pdb
---
warnings | Start residue of secondary structure not found: HELIX 8 AA8 THR I 28 TYR I 32 5 5
Start residue of secondary structure not found: HELIX 9 AA9 ASN I 73 LYS I 75
5 3
Start residue of secondary structure not found: HELIX 10 AB1 LYS I 83 THR I 87
5 5
Start residue of secondary structure not found: HELIX 11 AB2 SER I 156 SER I
158 5 3
Start residue of secondary structure not found: HELIX 12 AB3 PRO I 200 SER I
203 5 4
49 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (22 )
Cannot find LINK/SSBOND residue CYS (128 )
Cannot find LINK/SSBOND residue CYS (140 )
Cannot find LINK/SSBOND residue CYS (24 )
Cannot find LINK/SSBOND residue CYS (135 )
3C11_Fab_D_1292144377_model-annotate_P1_HL-coot-0.pdb title:
Fab fragment of an antibody that recognises all conformations of
α-1-antitrypsin [more info...]
Chain information for 3C11_Fab_D_1292144377_model-annotate_P1_HL-coot-0.pdb #4
---
Chain | Description
H | fab 3C11 heavy chain
L | fab 3C11 light chain
128 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Chain information for 1ezx_moved-coot-0.pdb #5
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> save /Users/apple/Downloads/csparc.cxs includeMaps true
> open /Users/apple/Downloads/3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb
Summary of feedback from opening
/Users/apple/Downloads/3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb
---
warnings | Start residue of secondary structure not found: HELIX 8 AA8 THR I 28 TYR I 32 5 5
Start residue of secondary structure not found: HELIX 9 AA9 ASN I 73 LYS I 75
5 3
Start residue of secondary structure not found: HELIX 10 AB1 LYS I 83 THR I 87
5 5
Start residue of secondary structure not found: HELIX 11 AB2 SER I 156 SER I
158 5 3
Start residue of secondary structure not found: HELIX 12 AB3 PRO I 200 SER I
203 5 4
49 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (22 )
Cannot find LINK/SSBOND residue CYS (128 )
Cannot find LINK/SSBOND residue CYS (140 )
Cannot find LINK/SSBOND residue CYS (24 )
Cannot find LINK/SSBOND residue CYS (135 )
3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb title:
Fab fragment of an antibody that recognises all conformations of
α-1-antitrypsin [more info...]
Chain information for 3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb #6
---
Chain | Description
H | fab 3C11 heavy chain
L | fab 3C11 light chain
128 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> mmaker #6 to #4
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3C11_Fab_D_1292144377_model-annotate_P1_HL-coot-0.pdb, chain L (#4)
with 3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb, chain L (#6), sequence
alignment score = 1108.5
RMSD between 208 pruned atom pairs is 0.000 angstroms; (across all 208 pairs:
0.000)
> hide #!4 models
> save /Users/apple/Downloads/csparc.cxs includeMaps true
> open /Users/apple/Downloads/cryosparc_P371_J891_003_volume_map.mrc
Opened cryosparc_P371_J891_003_volume_map.mrc as #7, grid size 300,300,300,
pixel 0.867, shown at level 0.0162, step 2, values float32
> volume #7 level 0.0734
> select subtract #3
Nothing selected
> hide #5 models
> hide #!6 models
> volume #7 level 0.05238
> hide #!7 models
> show #!6 models
> show #5 models
> show #!3 models
> show #!7 models
> hide #!7 models
> open "/Users/apple/Downloads/cryosparc_P371_J882_005_volume_map (1).mrc"
Opened cryosparc_P371_J882_005_volume_map (1).mrc as #8, grid size
300,300,300, pixel 0.867, shown at level 0.0235, step 2, values float32
> hide #5 models
> hide #!6 models
> volume #8 level 0.0555
> volume flip #8 axis z
Opened cryosparc_P371_J882_005_volume_map (1).mrc z flip as #9, grid size
300,300,300, pixel 0.867, shown at step 1, values float32
> volume #9 level 0.06023
> show #!1 models
> hide #!1 models
> show #5 models
> hide #5 models
> volume copy #5
> show #5 models
> hide #5 models
> show #!1 models
> transparency #8 50
> transparency #9 50
> show #!4 models
> hide #!4 models
> show #!6 models
> close #8
> show #!7 models
> hide #!7 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> open /Users/apple/Downloads/cryosparc_P371_J881_class_08_00006_volume.mrc
Opened cryosparc_P371_J881_class_08_00006_volume.mrc as #8, grid size
180,180,180, pixel 1.44, shown at level 0.0542, step 1, values float32
> volume #8 level 0.122
> volume flip #8 axis z
Opened cryosparc_P371_J881_class_08_00006_volume.mrc z flip as #10, grid size
180,180,180, pixel 1.44, shown at step 1, values float32
> select down
Nothing selected
> select down
Nothing selected
> transparency #8 50
> transparency #10 50
> hide #!10 models
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> close #8
> show #!7 models
> hide #!7 models
> close #7
> save /Users/apple/Downloads/csparc.cxs includeMaps true
——— End of log from Tue Nov 25 15:20:48 2025 ———
opened ChimeraX session
> show #!3 models
> open 5A0C fromDatabase pdb format mmcif
5a0c title:
Crystal Structure of human neutrophil elastase in complex with a
dihydropyrimidone inhibitor [more info...]
Chain information for 5a0c #7
---
Chain | Description | UniProt
A B | NEUTROPHIL ELASTASE | ELNE_HUMAN 16-252
Non-standard residues in 5a0c #7
---
FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose;
L-fucose; fucose)
JJV — (6S)-6-(4-cyano-2-methylsulfonyl-
phenyl)-4-methyl-2-oxidanylidene-3-[3-(trifluoromethyl)phenyl]-1,6-dihydropyrimidine-5-carbonitrile
MES — 2-(N-morpholino)-ethanesulfonic acid
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
XPE — 3,6,9,12,15,18,21,24,27-nonaoxanonacosane-1,29-diol (decaethylene
glycol)
5a0c mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> hide #!1 models
> show #!1 models
> open 1ezx fromDatabase pdb format mmcif
1ezx title:
Crystal structure of A serpin:protease complex [more info...]
Chain information for 1ezx #8
---
Chain | Description | UniProt
A | ALPHA-1-ANTITRYPSIN | A1AT_HUMAN 24-358
B | ALPHA-1-ANTITRYPSIN | A1AT_HUMAN 359-394
C | TRYPSIN | TRY1_BOVIN 42-245
> select #8/A
2686 atoms, 2674 bonds, 398 residues, 1 model selected
> mmaker #8 to #1
Computing secondary structure
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 1ezx, chain A (#1) with 1ezx, chain A (#8), sequence alignment
score = 1734
RMSD between 335 pruned atom pairs is 0.000 angstroms; (across all 335 pairs:
0.000)
> select #7/B, C, D, E, F
1965 atoms, 1848 bonds, 391 residues, 1 model selected
> delete #7/B, C, D, E, F
> mmaker #7 to #8
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1ezx, chain C (#8) with 5a0c, chain A (#7), sequence alignment
score = 241.2
RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
3.073)
> hide #7#!1,6,8 atoms
> save /Users/apple/Downloads/csparc.cxs includeMaps true
> open /Users/apple/Downloads/cryosparc_P371_J916_map.mrc
Opened cryosparc_P371_J916_map.mrc as #11, grid size 300,300,300, pixel 0.867,
shown at level 0.0238, step 2, values float32
> volume flip #11 axis z
Opened cryosparc_P371_J916_map.mrc z flip as #12, grid size 300,300,300, pixel
0.867, shown at step 1, values float32
> volume #12 level 0.06229
> transparency #12 50
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!6 models
> show #!6 models
> hide #!8 models
> show #!8 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #7 models
> show #7 models
> hide #!8 models
> ui tool show "Fit in Map"
> fitmap #7 inMap #12
Fit molecule 5a0c (#7) to map cryosparc_P371_J916_map.mrc z flip (#12) using
1883 atoms
average map value = 0.05726, steps = 204
shifted from previous position = 18.9
rotated from previous position = 30.2 degrees
atoms outside contour = 1095, contour level = 0.06229
Position of 5a0c (#7) relative to cryosparc_P371_J916_map.mrc z flip (#12)
coordinates:
Matrix rotation and translation
-0.89591156 -0.08748371 -0.43553310 147.09781032
0.42229009 -0.47204043 -0.77385329 138.97672191
-0.13788968 -0.87722542 0.45984998 149.26233444
Axis -0.17249142 -0.49666131 0.85063168
Axis point 74.69777418 126.82872456 0.00000000
Rotation angle (degrees) 162.56376196
Shift along axis 32.56979814
> show #!1 models
> hide #7 models
> show #7 models
> volume #11 level 0.05033
> volume #12 level 0.08057
> open /Users/apple/Downloads/cryosparc_P371_J919_class_00_final_volume.mrc
Opened cryosparc_P371_J919_class_00_final_volume.mrc as #13, grid size
128,128,128, pixel 2.03, shown at level 0.08, step 1, values float32
> transparency #18 50
> transparency #13 50
> hide #!13 models
> hide #7 models
> hide #!6 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> hide #!1 models
> show #7 models
> show #!8 models
> hide #!8 models
> show #!1 models
> show #!13 models
> show #!4 models
> hide #!4 models
> show #5 models
> hide #5 models
> show #!6 models
> hide #!6 models
> save /Users/apple/Downloads/csparc.cxs includeMaps true
——— End of log from Fri Nov 28 18:17:17 2025 ———
opened ChimeraX session
> hide #!13 models
> open /Users/apple/Downloads/cryosparc_P371_J937_003_volume_map.mrc
Opened cryosparc_P371_J937_003_volume_map.mrc as #14, grid size 300,300,300,
pixel 0.867, shown at level 0.0245, step 2, values float32
> volume flip #14 axis z
Opened cryosparc_P371_J937_003_volume_map.mrc z flip as #15, grid size
300,300,300, pixel 0.867, shown at step 1, values float32
> hide #!15 models
> hide #!1 models
> show #!1 models
> combine #1 close false
> hide #!1 models
> show #!6 models
> combine #6 close false
> combine #7 close false
> hide #7 models
> hide #!6 models
> hide #!3 models
> show #!15 models
> transparency #15 50
> volume #15 level 0.07742
> hide #!17 models
> hide #18 models
> hide #!16 models
> show #!16 models
> show #!17 models
> show #18 models
> select add #16
2975 atoms, 2968 bonds, 437 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.38245,0.10992,-0.91742,194.95,0.077506,-0.98558,-0.15039,187,-0.92072,-0.12862,0.36841,167.53
> view matrix models
> #16,-0.38245,0.10992,-0.91742,191.4,0.077506,-0.98558,-0.15039,187.17,-0.92072,-0.12862,0.36841,156.11
> view matrix models
> #16,-0.014922,0.064965,-0.99778,175.36,0.069994,-0.99537,-0.065855,183.33,-0.99744,-0.070821,0.010305,178.28
> hide #!17 models
> view matrix models
> #16,-0.014922,0.064965,-0.99778,182.37,0.069994,-0.99537,-0.065855,183.4,-0.99744,-0.070821,0.010305,175.03
> view matrix models
> #16,0.94124,0.016979,-0.33731,85.904,0.1062,-0.96295,0.24788,160.88,-0.32061,-0.26914,-0.90817,197.31
> view matrix models
> #16,0.6158,0.19853,0.76248,31.693,-0.013436,-0.96495,0.26209,167.81,0.78779,-0.17164,-0.59155,102.23
> view matrix models
> #16,-0.056736,0.045988,0.99733,70.269,-0.1345,-0.99018,0.038008,190.1,0.98929,-0.13198,0.062364,48.953
> view matrix models
> #16,-0.056736,0.045988,0.99733,68.694,-0.1345,-0.99018,0.038008,189.37,0.98929,-0.13198,0.062364,47.206
> ui tool show "Fit in Map"
> fitmap #16 inMap #15
Fit molecule copy of 1ezx (#16) to map cryosparc_P371_J937_003_volume_map.mrc
z flip (#15) using 2975 atoms
average map value = 0.08682, steps = 136
shifted from previous position = 1.54
rotated from previous position = 27.4 degrees
atoms outside contour = 1268, contour level = 0.077423
Position of copy of 1ezx (#16) relative to
cryosparc_P371_J937_003_volume_map.mrc z flip (#15) coordinates:
Matrix rotation and translation
0.36221471 -0.11330418 0.92518250 57.47272519
-0.01922981 -0.99328137 -0.11411544 191.48317940
0.93189630 0.02354321 -0.36195994 67.99746912
Axis 0.82495481 -0.04023415 0.56376482
Axis point 0.00000000 96.53522281 19.29015841
Rotation angle (degrees) 175.21401689
Shift along axis 78.04281848
> show #!17 models
> select subtract #16
Nothing selected
> select add #17
3190 atoms, 3270 bonds, 2 pseudobonds, 422 residues, 3 models selected
> view matrix models
> #17,-0.14524,0.98625,-0.078838,137.46,-0.95305,-0.11806,0.27883,132.77,0.26569,0.11563,0.9571,127.09
> view matrix models
> #17,0.35108,0.87998,0.31997,116.61,0.41428,-0.45244,0.78973,93.952,0.83971,-0.14471,-0.5234,164.49
> view matrix models
> #17,0.54911,0.70874,-0.44291,137.73,0.78853,-0.61496,-0.0064507,113,-0.27694,-0.3457,-0.89655,196.5
> view matrix models
> #17,0.54911,0.70874,-0.44291,134.48,0.78853,-0.61496,-0.0064507,113.87,-0.27694,-0.3457,-0.89655,190.34
> view matrix models
> #17,0.9378,-0.11961,-0.32592,126.95,-0.057609,-0.97937,0.19367,123.71,-0.34236,-0.16285,-0.92535,191.74
> view matrix models
> #17,0.3628,-0.93186,-0.0012508,129.72,-0.91856,-0.35785,0.16792,137.38,-0.15693,-0.059774,-0.9858,190.03
> view matrix models
> #17,-0.40726,-0.90893,0.089337,140.28,-0.91297,0.40784,-0.012447,140.22,-0.025122,-0.086631,-0.99592,188.13
> view matrix models
> #17,-0.40726,-0.90893,0.089337,140.76,-0.91297,0.40784,-0.012447,134.78,-0.025122,-0.086631,-0.99592,187.94
> view matrix models
> #17,-0.073903,-0.92576,-0.37083,149.44,-0.76049,-0.18823,0.62147,114.32,-0.64513,0.32794,-0.69012,187.71
> view matrix models
> #17,-0.013726,-0.97437,-0.22454,143.96,-0.96969,-0.041822,0.24075,129.42,-0.24397,0.22104,-0.94426,189.05
> view matrix models
> #17,-0.13546,-0.99065,0.016086,138.59,-0.95193,0.13463,0.27516,127.4,-0.27475,0.02196,-0.96126,190.84
> view matrix models
> #17,-0.13546,-0.99065,0.016086,134.75,-0.95193,0.13463,0.27516,129.71,-0.27475,0.02196,-0.96126,190.41
> view matrix models
> #17,-0.13546,-0.99065,0.016086,134.74,-0.95193,0.13463,0.27516,129.59,-0.27475,0.02196,-0.96126,189.59
> fitmap #17 inMap #15
Fit molecule copy of 3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb (#17) to
map cryosparc_P371_J937_003_volume_map.mrc z flip (#15) using 3190 atoms
average map value = 0.08611, steps = 92
shifted from previous position = 1.81
rotated from previous position = 13.7 degrees
atoms outside contour = 1360, contour level = 0.077423
Position of copy of 3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb (#17)
relative to cryosparc_P371_J937_003_volume_map.mrc z flip (#15) coordinates:
Matrix rotation and translation
0.06326154 -0.99140205 0.11454237 128.16146514
-0.92943347 -0.01671960 0.36861077 128.17971107
-0.36352637 -0.12977839 -0.92249995 190.93357303
Axis -0.71877784 0.68947168 0.08937122
Axis point 0.00000000 149.17005870 88.62629203
Rotation angle (degrees) 159.71487953
Shift along axis 13.32062667
> select subtract #17
Nothing selected
> select add #18
1883 atoms, 1745 bonds, 394 residues, 1 model selected
> view matrix models
> #18,-0.26486,0.8524,-0.45085,130.11,0.42774,-0.31518,-0.84718,156.88,-0.86423,-0.41723,-0.28112,157.69
> view matrix models
> #18,-0.26486,0.8524,-0.45085,127.04,0.42774,-0.31518,-0.84718,159.13,-0.86423,-0.41723,-0.28112,133.82
> view matrix models
> #18,0.36105,0.83492,0.4154,114.71,0.60304,0.13074,-0.78692,152.96,-0.71132,0.53462,-0.45629,125.04
> show #!8 models
> select up
26260 atoms, 26186 bonds, 3972 residues, 27 models selected
> select up
26260 atoms, 26186 bonds, 3972 residues, 27 models selected
> select down
1883 atoms, 1745 bonds, 394 residues, 1 model selected
> select down
1883 atoms, 1745 bonds, 394 residues, 1 model selected
> combine #8 close false
> hide #!8 models
> select subtract #18
Nothing selected
> mmaker #19 to #16
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 copy of 1ezx, chain A (#16) with copy of 1ezx, chain A (#19),
sequence alignment score = 1734
RMSD between 335 pruned atom pairs is 0.000 angstroms; (across all 335 pairs:
0.000)
> hide #!16 models
> show #!16 models
> mmaker #18 to #19
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 copy of 1ezx, chain C (#19) with copy of 5a0c, chain A (#18),
sequence alignment score = 241.2
RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
3.073)
> hide #!19 models
> show #!19 models
> hide #18 models
> show #18 models
> hide #!15 models
> show #!15 models
> volume #15 level 0.06266
> combine #18 close false
> hide #!19 models
> hide #18 models
> select add #20
1883 atoms, 1745 bonds, 394 residues, 1 model selected
> view matrix models
> #20,0.93703,-0.32924,0.11649,110.54,-0.085791,-0.54033,-0.83707,168.71,0.33854,0.77436,-0.53456,110.95
> fitmap #20 inMap #15
Fit molecule copy of copy of 5a0c (#20) to map
cryosparc_P371_J937_003_volume_map.mrc z flip (#15) using 1883 atoms
average map value = 0.05371, steps = 112
shifted from previous position = 3.05
rotated from previous position = 21.1 degrees
atoms outside contour = 1163, contour level = 0.062657
Position of copy of copy of 5a0c (#20) relative to
cryosparc_P371_J937_003_volume_map.mrc z flip (#15) coordinates:
Matrix rotation and translation
0.82283210 -0.54792418 -0.15075286 115.81404414
-0.42467040 -0.41658213 -0.80381240 174.25196583
0.37762731 0.72542292 -0.57546433 108.00195017
Axis 0.94244068 -0.32563135 0.07595913
Axis point 0.00000000 79.04749924 102.02767242
Rotation angle (degrees) 125.77524387
Shift along axis 60.60969773
> volume #15 level 0.07496
> volume #15 level 0.102
> fitmap #20 inMap #15
Fit molecule copy of copy of 5a0c (#20) to map
cryosparc_P371_J937_003_volume_map.mrc z flip (#15) using 1883 atoms
average map value = 0.05371, steps = 40
shifted from previous position = 0.00581
rotated from previous position = 0.0038 degrees
atoms outside contour = 1822, contour level = 0.10203
Position of copy of copy of 5a0c (#20) relative to
cryosparc_P371_J937_003_volume_map.mrc z flip (#15) coordinates:
Matrix rotation and translation
0.82283660 -0.54793499 -0.15068899 115.81020155
-0.42463523 -0.41661833 -0.80381222 174.25584664
0.37765705 0.72539397 -0.57548131 108.00286277
Axis 0.94244310 -0.32561736 0.07598910
Axis point 0.00000000 79.04924478 102.02529443
Rotation angle (degrees) 125.77696296
Shift along axis 60.61083741
> volume #15 level 0.08481
> select #20/Ser195
Nothing selected
> ui tool show "Show Sequence Viewer"
> sequence chain #7/A #18/A #20/A
Alignment identifier is 1
> select #7/A:157 #18/A:157 #20/A:157
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #7/A:157 #18/A:157 #20/A:157
18 atoms, 15 bonds, 3 residues, 3 models selected
NEUTROPHIL ELASTASE [ID: 1] region 3 chains [138] RMSD: 42.465
> show #18 models
> hide #20 models
> select #7/A:157 #18/A:157 #20/A:157
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #7/A:157 #18/A:157 #20/A:157
18 atoms, 15 bonds, 3 residues, 3 models selected
NEUTROPHIL ELASTASE [ID: 1] region 3 chains [138] RMSD: 42.465
> select #7/A:195 #18/A:195 #20/A:195
15 atoms, 12 bonds, 3 residues, 3 models selected
> select #7/A:195 #18/A:195 #20/A:195
15 atoms, 12 bonds, 3 residues, 3 models selected
NEUTROPHIL ELASTASE [ID: 1] region 3 chains [166] RMSD: 29.400
> show #!19 models
> hide #!15 models
> select #7/A:195 #18/A:195 #20/A:195
15 atoms, 12 bonds, 3 residues, 3 models selected
> select #7/A:195 #18/A:195 #20/A:195
15 atoms, 12 bonds, 3 residues, 3 models selected
> select #7/A:195-198 #18/A:195-198 #20/A:195-198
66 atoms, 63 bonds, 12 residues, 3 models selected
NEUTROPHIL ELASTASE [ID: 1] region 3 chains [166-169] RMSD: 25.331
> select #7/A:196 #18/A:196 #20/A:196
12 atoms, 9 bonds, 3 residues, 3 models selected
> select #7/A:195-196 #18/A:195-196 #20/A:195-196
27 atoms, 24 bonds, 6 residues, 3 models selected
NEUTROPHIL ELASTASE [ID: 1] region 3 chains [166-167] RMSD: 26.853
> hide #18 models
> ui tool show "Show Sequence Viewer"
> sequence chain #8/C #19/C
Alignment identifier is 2
> select #7/A:202 #18/A:202 #20/A:202
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #7/A:202 #18/A:202 #20/A:202
18 atoms, 15 bonds, 3 residues, 3 models selected
NEUTROPHIL ELASTASE [ID: 1] region 3 chains [173] RMSD: 20.338
> show #18 models
> hide #!19 models
> show #20 models
> hide #18 models
> show #!15 models
> fitmap #20 inMap #15
Fit molecule copy of copy of 5a0c (#20) to map
cryosparc_P371_J937_003_volume_map.mrc z flip (#15) using 1883 atoms
average map value = 0.05371, steps = 44
shifted from previous position = 0.00953
rotated from previous position = 0.0167 degrees
atoms outside contour = 1647, contour level = 0.084806
Position of copy of copy of 5a0c (#20) relative to
cryosparc_P371_J937_003_volume_map.mrc z flip (#15) coordinates:
Matrix rotation and translation
0.82274117 -0.54810241 -0.15060115 115.80769501
-0.42459237 -0.41645168 -0.80392121 174.26154718
0.37791306 0.72536318 -0.57535204 108.00158372
Axis 0.94240739 -0.32569200 0.07611192
Axis point 0.00000000 79.05386504 102.02910751
Rotation angle (degrees) 125.76988347
Shift along axis 60.60264436
> save /Users/apple/Downloads/csparc.cxs
> show #!19 models
> hide #20 models
> show #20 models
> hide #!19 models
> save /Users/apple/Downloads/csparc.cxs includeMaps true
> open /Users/apple/Downloads/cryosparc_P371_J936_volume_map.mrc
Opened cryosparc_P371_J936_volume_map.mrc as #21, grid size 300,300,300, pixel
0.867, shown at level 0.0323, step 2, values float32
> volume #21 level 0.05076
> volume flip #21 axis z
Opened cryosparc_P371_J936_volume_map.mrc z flip as #22, grid size
300,300,300, pixel 0.867, shown at step 1, values float32
> transparency #22 50
> volume #22 level 0.08397
> hide #!15 models
> hide #!22 models
> show #!22 models
> volume #22 level 0.09518
> select add #21
18 atoms, 15 bonds, 3 residues, 5 models selected
> select subtract #21
18 atoms, 15 bonds, 3 residues, 3 models selected
> close #21-22
> show #!15 models
> volume #15 level 0.06828
> show #!19 models
> hide #!19 models
> show #!19 models
> select up
309 atoms, 309 bonds, 45 residues, 3 models selected
> select up
4908 atoms, 5010 bonds, 654 residues, 3 models selected
> select down
309 atoms, 309 bonds, 45 residues, 3 models selected
> select down
18 atoms, 15 bonds, 3 residues, 3 models selected
> mmaker #20 to #19
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 copy of 1ezx, chain C (#19) with copy of copy of 5a0c, chain A
(#20), sequence alignment score = 241.2
RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
3.073)
> fitmap #20 inMap #15
Fit molecule copy of copy of 5a0c (#20) to map
cryosparc_P371_J937_003_volume_map.mrc z flip (#15) using 1883 atoms
average map value = 0.05371, steps = 112
shifted from previous position = 3.64
rotated from previous position = 21.1 degrees
atoms outside contour = 1322, contour level = 0.068282
Position of copy of copy of 5a0c (#20) relative to
cryosparc_P371_J937_003_volume_map.mrc z flip (#15) coordinates:
Matrix rotation and translation
0.82286685 -0.54787123 -0.15075561 115.81112827
-0.42466982 -0.41665469 -0.80377510 174.25405615
0.37755223 0.72542124 -0.57551571 108.00346093
Axis 0.94245398 -0.32559967 0.07592986
Axis point 0.00000000 79.04723098 102.02619388
Rotation angle (degrees) 125.77839312
Shift along axis 60.61028363
> hide #!19 models
> show #18 models
> hide #18 models
> color #20 #ff9cd5ff
> open /Users/apple/Downloads/cryosparc_P371_J948_003_volume_map.mrc
Opened cryosparc_P371_J948_003_volume_map.mrc as #21, grid size 300,300,300,
pixel 0.867, shown at level 0.0208, step 2, values float32
> volume flip #21 axis z
Opened cryosparc_P371_J948_003_volume_map.mrc z flip as #22, grid size
300,300,300, pixel 0.867, shown at step 1, values float32
> select add #22
18 atoms, 15 bonds, 3 residues, 5 models selected
> select subtract #22
18 atoms, 15 bonds, 3 residues, 3 models selected
> hide #20 models
> show #20 models
> hide #20 models
> show #20 models
> hide #20 models
> hide #!17 models
> hide #!16 models
> select add #18
1895 atoms, 1755 bonds, 396 residues, 3 models selected
> select subtract #18
12 atoms, 10 bonds, 2 residues, 2 models selected
> select add #20
1889 atoms, 1750 bonds, 395 residues, 2 models selected
> select subtract #20
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #7
1883 atoms, 1745 bonds, 394 residues, 1 model selected
> select subtract #7
Nothing selected
> volume #22 level 0.07591
> select down
Nothing selected
> combine #16 close false
> combine #17 close false
> combine #118 close false
No structures specified
> combine #18 close false
> combine #19 close false
> transparency #22 50
> hide #!26 models
> hide #25 models
> hide #!24 models
> select add #23
2975 atoms, 2968 bonds, 437 residues, 1 model selected
> view matrix models
> #23,0.36221,-0.1133,0.92518,56.114,-0.01923,-0.99328,-0.11412,190.58,0.9319,0.023543,-0.36196,109.58
> view matrix models
> #23,0.36479,-0.4655,-0.80637,178.05,-0.26782,-0.88191,0.38795,170.47,-0.89174,0.074435,-0.44638,227.76
> view matrix models
> #23,0.44719,-0.25874,-0.8562,163.07,-0.021132,-0.96003,0.27908,165.82,-0.89419,-0.10671,-0.43478,238.29
> fitmap #23 inMap #22
Fit molecule copy of copy of 1ezx (#23) to map
cryosparc_P371_J948_003_volume_map.mrc z flip (#22) using 2975 atoms
average map value = 0.09755, steps = 212
shifted from previous position = 6.95
rotated from previous position = 52.1 degrees
atoms outside contour = 1049, contour level = 0.075909
Position of copy of copy of 1ezx (#23) relative to
cryosparc_P371_J948_003_volume_map.mrc z flip (#22) coordinates:
Matrix rotation and translation
-0.35370767 0.06701706 -0.93295209 204.77529060
0.13164154 -0.98393545 -0.12058828 178.13445921
-0.92604610 -0.16546825 0.33920329 197.74865607
Axis -0.56822714 -0.08743693 0.81821311
Axis point 168.87143840 102.30996261 0.00000000
Rotation angle (degrees) 177.73673097
Shift along axis 29.86613558
> show #!24 models
> select subtract #23
Nothing selected
> select add #24
3190 atoms, 3270 bonds, 2 pseudobonds, 422 residues, 3 models selected
> view matrix models
> #24,0.063262,-0.9914,0.11454,130.74,-0.92943,-0.01672,0.36861,129.85,-0.36353,-0.12978,-0.9225,142.93
> view matrix models
> #24,-0.096416,0.97724,-0.18895,136.05,-0.93565,-0.024237,0.35209,130.5,0.33949,0.21074,0.9167,71.599
> fitmap #24 inMap #22
Fit molecule copy of copy of 3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb
(#24) to map cryosparc_P371_J948_003_volume_map.mrc z flip (#22) using 3190
atoms
average map value = 0.0891, steps = 132
shifted from previous position = 5.66
rotated from previous position = 8.17 degrees
atoms outside contour = 1367, contour level = 0.075909
Position of copy of copy of 3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb
(#24) relative to cryosparc_P371_J948_003_volume_map.mrc z flip (#22)
coordinates:
Matrix rotation and translation
-0.11543452 0.98844688 -0.09822239 132.09657369
-0.96240593 -0.08681878 0.25736612 135.79332431
0.24586519 0.12423874 0.96130902 66.63288452
Axis -0.06705205 -0.17330603 -0.98258284
Axis point 117.34974721 5.42399614 0.00000000
Rotation angle (degrees) 96.91935179
Shift along axis -97.86347693
> select subtract #24
Nothing selected
> show #25 models
> hide #25 models
> show #!26 models
> mmaker #26 to #23
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 copy of copy of 1ezx, chain A (#23) with copy of copy of 1ezx,
chain A (#26), sequence alignment score = 1734
RMSD between 335 pruned atom pairs is 0.000 angstroms; (across all 335 pairs:
0.000)
> hide #!24 models
> show #!24 models
> hide #!23 models
> show #25 models
> mmaker #25 to #26
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 copy of copy of 1ezx, chain C (#26) with copy of copy of 5a0c,
chain A (#25), sequence alignment score = 241.2
RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
3.073)
> hide #!26 models
> fitmap #25 inMap #22
Fit molecule copy of copy of 5a0c (#25) to map
cryosparc_P371_J948_003_volume_map.mrc z flip (#22) using 1883 atoms
average map value = 0.05123, steps = 108
shifted from previous position = 4.84
rotated from previous position = 10.8 degrees
atoms outside contour = 1517, contour level = 0.075909
Position of copy of copy of 5a0c (#25) relative to
cryosparc_P371_J948_003_volume_map.mrc z flip (#22) coordinates:
Matrix rotation and translation
-0.96845122 0.24832236 -0.02093422 151.81572996
-0.06074205 -0.31669183 -0.94658158 164.61638030
-0.24168707 -0.91544650 0.32178420 153.13479473
Axis 0.08170221 0.57928205 -0.81102223
Axis point 93.94357397 127.91849703 0.00000000
Rotation angle (degrees) 169.01569846
Shift along axis -16.43272779
> select add #25
1883 atoms, 1745 bonds, 394 residues, 1 model selected
> view matrix models
> #25,-0.77469,0.63129,-0.036468,145.91,-0.26885,-0.38101,-0.88462,168.48,-0.57235,-0.6755,0.46489,156.84
> select subtract #25
Nothing selected
> show #!26 models
> hide #!24 models
> show #!24 models
> hide #25 models
> mmaker #25 to #26
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 copy of copy of 1ezx, chain C (#26) with copy of copy of 5a0c,
chain A (#25), sequence alignment score = 241.2
RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
3.073)
> hide #!26 models
> show #25 models
> show #!26 models
> mmaker #25 to #26
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 copy of copy of 1ezx, chain C (#26) with copy of copy of 5a0c,
chain A (#25), sequence alignment score = 241.2
RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
3.073)
> show #!23 models
> hide #!23 models
> hide #!26 models
> hide #25 models
> show #!26 models
> hide #!26 models
> show #25 models
> hide #25 models
> show #25 models
> show #!26 models
> select add #25
1883 atoms, 1745 bonds, 394 residues, 1 model selected
> view matrix models
> #25,-0.9367,0.31111,-0.16061,148.23,0.0082594,-0.43896,-0.89847,161.81,-0.35002,-0.84292,0.40861,148.72
> mmaker #25 to #26
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 copy of copy of 1ezx, chain C (#26) with copy of copy of 5a0c,
chain A (#25), sequence alignment score = 241.2
RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
3.073)
> hide #!22 models
> hide #!26 models
> select subtract #25
Nothing selected
> show #!22 models
> hide #!22 models
> show #!26 models
> hide #25 models
> show #25 models
> hide #25 models
> show #25 models
> select add #25
1883 atoms, 1745 bonds, 394 residues, 1 model selected
> view matrix models
> #25,-0.9367,0.31111,-0.16061,148.98,0.0082594,-0.43896,-0.89847,185.49,-0.35002,-0.84292,0.40861,135.78
> view matrix models
> #25,-0.94082,0.30916,-0.13882,149.02,0.0018899,-0.40484,-0.91439,185.4,-0.33889,-0.86054,0.3803,135.77
> view matrix models
> #25,-0.94082,0.30916,-0.13882,149.87,0.0018899,-0.40484,-0.91439,185.44,-0.33889,-0.86054,0.3803,134.62
> view matrix models
> #25,0.61831,0.086644,0.78114,122.91,0.644,0.51386,-0.56675,167.46,-0.45051,0.85348,0.26193,124.99
> view matrix models
> #25,0.68702,0.1216,0.7164,121.63,0.51681,0.61128,-0.59937,169.03,-0.5108,0.78202,0.35712,126.32
> view matrix models
> #25,-0.95703,-0.21929,0.18975,153.1,-0.15891,-0.15078,-0.97571,186.56,0.24258,-0.96394,0.10945,125.96
> select #8/C:202 #19/C:202
12 atoms, 10 bonds, 2 residues, 2 models selected
> select #8/C:202 #19/C:202
12 atoms, 10 bonds, 2 residues, 2 models selected
TRYPSIN [ID: 2] region 2 chains [204] RMSD: 14.654
> select #8/C:195 #19/C:195
12 atoms, 10 bonds, 2 residues, 2 models selected
> select #8/C:195 #19/C:195
12 atoms, 10 bonds, 2 residues, 2 models selected
TRYPSIN [ID: 2] region 2 chains [197] RMSD: 26.141
> select #7/A:202 #18/A:202 #20/A:202
18 atoms, 15 bonds, 3 residues, 3 models selected
> select #7/A:202 #18/A:202 #20/A:202
18 atoms, 15 bonds, 3 residues, 3 models selected
NEUTROPHIL ELASTASE [ID: 1] region 3 chains [173] RMSD: 20.338
> show #20 models
> hide #20 models
> select #25/A Ser 202
Expected a keyword
> select #25/A:Ser 202
Expected a keyword
> select #25/A:Ser202
Nothing selected
> select #25: 202.A
Expected an objects specifier or a keyword
> select #25/A: 202
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #25
1883 atoms, 1745 bonds, 394 residues, 1 model selected
> select subtract #25
Nothing selected
> select add #25
1883 atoms, 1745 bonds, 394 residues, 1 model selected
> hide #!26 models
> show #!22 models
> show #!21 models
> hide #!21 models
> show #!23 models
> view matrix models
> #25,-0.95703,-0.21929,0.18975,145.87,-0.15891,-0.15078,-0.97571,168.63,0.24258,-0.96394,0.10945,142.99
> view matrix models
> #25,-0.92453,-0.26838,-0.2706,146.59,0.26503,0.057502,-0.96252,159.94,0.27389,-0.96159,0.017967,142.62
> select #25/A: 202
6 atoms, 5 bonds, 1 residue, 1 model selected
> fitmap #25 inMap #22
Fit molecule copy of copy of 5a0c (#25) to map
cryosparc_P371_J948_003_volume_map.mrc z flip (#22) using 1883 atoms
average map value = 0.05191, steps = 80
shifted from previous position = 6.32
rotated from previous position = 2.92 degrees
atoms outside contour = 1497, contour level = 0.075909
Position of copy of copy of 5a0c (#25) relative to
cryosparc_P371_J948_003_volume_map.mrc z flip (#22) coordinates:
Matrix rotation and translation
-0.92706110 -0.29700612 -0.22879047 151.40778359
0.22401549 0.05050483 -0.97327608 156.79876717
0.30062397 -0.95353900 0.01971291 143.82999540
Axis 0.02656202 -0.71248224 0.70118722
Axis point 58.53175465 0.00000000 169.56684388
Rotation angle (degrees) 158.19010570
Shift along axis -6.84288466
> hide #!22 models
> show #!22 models
> view
> ui mousemode right "tape measure"
> marker segment #27 position 135.4,127.7,167.7 toPosition 124.3,129.1,64.78
> color yellow radius 0.2167 label 103.5 labelHeight 10.35 labelColor yellow
> marker segment #27 position 125.5,89.39,147.8 toPosition 125.6,178.4,143.9
> color yellow radius 0.2167 label 89.07 labelHeight 8.907 labelColor yellow
> close #27
> save /Users/apple/Downloads/csparc.cxs includeMaps true
> open 1oph fromDatabase pdb format mmcif
1oph title:
Non-covalent complex between α-1-π-pittsburgh and S195A trypsin [more info...]
Chain information for 1oph #27
---
Chain | Description | UniProt
A | Alpha-1-antitrypsin precursor | A1AT_HUMAN 1-394
B | Trypsinogen, cationic precursor | TRY1_BOVIN -4-245
1oph mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| software_defined_assembly
> select #27/A
3121 atoms, 2980 bonds, 578 residues, 1 model selected
> delete #27/A
> mmaker #27 to #26
Computing secondary structure
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 copy of copy of 1ezx, chain C (#26) with 1oph, chain B (#27),
sequence alignment score = 997.3
RMSD between 122 pruned atom pairs is 0.798 angstroms; (across all 140 pairs:
2.232)
> show #!26 models
> hide #25 models
> hide #!26 models
> select add #27
1798 atoms, 1661 bonds, 397 residues, 1 model selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #27,-0.045437,0.97583,0.21376,84.546,-0.056484,-0.21614,0.97473,106.46,0.99737,0.032215,0.06494,111.78
> view matrix models
> #27,-0.045437,0.97583,0.21376,84.655,-0.056484,-0.21614,0.97473,107.21,0.99737,0.032215,0.06494,111.79
> view matrix models
> #27,-0.028766,0.99015,0.13706,88.816,-0.25704,-0.13983,0.95623,110.79,0.96597,-0.0077222,0.25853,101.15
> hide #27 models
> show #25 models
> show #27 models
> hide #25 models
> fitmap #27 inMap #22
Fit molecule 1oph (#27) to map cryosparc_P371_J948_003_volume_map.mrc z flip
(#22) using 1798 atoms
average map value = 0.05191, steps = 140
shifted from previous position = 5.08
rotated from previous position = 28.4 degrees
atoms outside contour = 1427, contour level = 0.075909
Position of 1oph (#27) relative to cryosparc_P371_J948_003_volume_map.mrc z
flip (#22) coordinates:
Matrix rotation and translation
0.00693020 0.97101511 -0.23891762 117.08280460
0.05673053 0.23815679 0.96956846 87.39953806
0.99836547 -0.02027323 -0.05343572 123.84959279
Axis -0.54108517 -0.67634607 -0.49978278
Axis point 8.31144747 0.00000000 37.97716599
Rotation angle (degrees) 113.83939914
Shift along axis -184.36199747
> ui tool show "Show Sequence Viewer"
> sequence chain #27/B
Alignment identifier is 27/B
> select #27/B:195
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #27/B:195
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide #27 models
> select add #27
1798 atoms, 1661 bonds, 397 residues, 1 model selected
> show #25 models
> show #!26 models
> hide #25 models
> hide #!26 models
> show #!26 models
> select up
45957 atoms, 45539 bonds, 7200 residues, 38 models selected
> select up
45957 atoms, 45539 bonds, 7200 residues, 38 models selected
> select down
1798 atoms, 1661 bonds, 397 residues, 1 model selected
> select down
1798 atoms, 1661 bonds, 397 residues, 1 model selected
> select down
1798 atoms, 1661 bonds, 397 residues, 1 model selected
> select #25/A: 202
6 atoms, 5 bonds, 1 residue, 1 model selected
> show #25 models
> hide #25 models
> select add #25
1883 atoms, 1745 bonds, 394 residues, 1 model selected
> select #26/B: 195
Nothing selected
> select #26/A: 195
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide #!22 models
> select #26/C: 195
6 atoms, 5 bonds, 1 residue, 1 model selected
> style sel ball
Changed 6 atom styles
> show sel atoms
> show #25 models
> hide #!26 models
> select #25/A: 202
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 6 atom styles
> style sel sphere
Changed 6 atom styles
> style sel ball
Changed 6 atom styles
> select add #25
1883 atoms, 1745 bonds, 394 residues, 1 model selected
> select subtract #25
Nothing selected
> select #23/A: 358
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 8 atom styles
> style sel stick
Changed 8 atom styles
> style sel ball
Changed 8 atom styles
> rainbow sel
> style sel ball
Changed 8 atom styles
> rainbow sel
> select add #23
2975 atoms, 2968 bonds, 437 residues, 1 model selected
> select subtract #23
Nothing selected
> show #!22 models
> hide #25 models
> show #!26 models
> hide #!26 models
> show #25 models
> hide #25 models
> volume #22 level 0.09375
> show #25 models
> hide #25 models
> show #!26 models
> hide #!26 models
> show #25 models
> hide #25 models
> open /Users/apple/Downloads/cryosparc_P371_J950_050_class_averages.mrc
Opened cryosparc_P371_J950_050_class_averages.mrc as #28, grid size
256,256,200, pixel 1.02,1.02,1.02, shown at level 0.251, step 1, values
float32
> close #28
> show #25 models
> select #25/A: 358
Nothing selected
> select #25/A: 202
6 atoms, 5 bonds, 1 residue, 1 model selected
> show #!26 models
> hide #!26 models
> hide #25 models
> hide #!24 models
> hide #!23 models
> show #!26 models
> hide #!22 models
> show #!22 models
> show #25 models
> hide #25 models
> hide #!26 models
> show #25 models
> show #!23 models
> ui mousemode right "mark center"
> marker #28 position 123.2,156.9,145.8 color yellow radius 1
> marker #28 position 123.8,156.1,145.9 color yellow radius 1
> marker #28 position 124.3,155.3,145.5 color yellow radius 1
> marker #28 position 125.1,154.7,145.3 color yellow radius 1
> marker #28 position 133.4,155.3,146.7 color yellow radius 1
> close #28
> marker #28 position 138.7,150.2,141.7 color yellow radius 1
> ui mousemode right "translate selected models"
> view matrix models #28,1,0,0,-3.5551,0,1,0,1.3867,0,0,1,-2.5059
> view matrix models #28,1,0,0,-9.6384,0,1,0,2.0334,0,0,1,1.97
> view matrix models #28,1,0,0,-10.982,0,1,0,2.5507,0,0,1,3.0554
> view matrix models #28,1,0,0,-10.831,0,1,0,1.6826,0,0,1,8.0306
> view matrix models #28,1,0,0,-9.3846,0,1,0,2.9816,0,0,1,8.0266
> view matrix models #28,1,0,0,-8.1692,0,1,0,2.6506,0,0,1,8.3086
> save /Users/apple/Downloads/csparc.cxs includeMaps true
——— End of log from Wed Dec 10 00:50:43 2025 ———
opened ChimeraX session
> open /Users/apple/Downloads/cryosparc_P371_J1081_flex_map.mrc
Opened cryosparc_P371_J1081_flex_map.mrc as #29, grid size 300,300,300, pixel
0.867, shown at level 0.000695, step 2, values float32
> open /Users/apple/Downloads/cryosparc_P371_J1081_noflex_map.mrc
Opened cryosparc_P371_J1081_noflex_map.mrc as #30, grid size 300,300,300,
pixel 0.867, shown at level 0.000724, step 2, values float32
> select subtract #28
Nothing selected
> hide #28 models
> hide #25 models
> hide #!23 models
> hide #!22 models
> volume #29 level 0.002147
> volume #30 level 0.002175
> volume #29 level 0.003511
> transparency #29 50
> combine #23 close false
> select #31
2975 atoms, 2968 bonds, 437 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #31,0.50304,0.85251,0.14206,39.723,-0.75321,0.51304,-0.41165,160.2,-0.42382,0.10008,0.9002,116.9
> view matrix models
> #31,-0.21174,-0.30564,-0.9283,218.18,-0.38185,0.90021,-0.2093,101.13,0.89964,0.31016,-0.30733,89.797
> view matrix models
> #31,-0.21174,-0.30564,-0.9283,229.13,-0.38185,0.90021,-0.2093,126.74,0.89964,0.31016,-0.30733,63.57
> view matrix models
> #31,-0.62266,-0.60519,-0.49602,248.5,-0.47185,0.79608,-0.37898,148.7,0.62422,-0.0019301,-0.78124,127.72
> view matrix models
> #31,-0.0049269,-0.1605,-0.98702,210.49,-0.17098,0.97264,-0.15731,105.85,0.98526,0.16799,-0.032234,50.793
> view matrix models
> #31,-0.0049269,-0.1605,-0.98702,193.82,-0.17098,0.97264,-0.15731,100.89,0.98526,0.16799,-0.032234,45.314
> ui tool show "Fit to Segments"
> ui tool show "Fit in Map"
> fitmap #31 inMap #29
Fit molecule copy of copy of copy of 1ezx (#31) to map
cryosparc_P371_J1081_flex_map.mrc (#29) using 2975 atoms
average map value = 0.00359, steps = 168
shifted from previous position = 8.5
rotated from previous position = 22.8 degrees
atoms outside contour = 1538, contour level = 0.003511
Position of copy of copy of copy of 1ezx (#31) relative to
cryosparc_P371_J1081_flex_map.mrc (#29) coordinates:
Matrix rotation and translation
-0.34543281 0.02159528 -0.93819498 206.18704506
-0.19036417 0.97733785 0.09258621 89.05596314
0.91893289 0.21058103 -0.33349359 58.61087565
Axis 0.06300096 -0.99157607 -0.11317149
Axis point 88.67581154 0.00000000 98.10599897
Rotation angle (degrees) 110.53590433
Shift along axis -81.94885947
> combine #26 close false
> mmaker #32 to #31
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 copy of copy of copy of 1ezx, chain A (#31) with copy of copy of
copy of 1ezx, chain A (#32), sequence alignment score = 1734
RMSD between 335 pruned atom pairs is 0.000 angstroms; (across all 335 pairs:
0.000)
> volume #29 level 0.003107
> hide #!32 models
> show #!32 models
> mmaker #27 to #32
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 copy of copy of copy of 1ezx, chain C (#32) with 1oph, chain B
(#27), sequence alignment score = 997.3
RMSD between 122 pruned atom pairs is 0.798 angstroms; (across all 140 pairs:
2.232)
> show #27 models
> select subtract #31
Nothing selected
> hide #!32 models
> fitmap #27 inMap #29
Fit molecule 1oph (#27) to map cryosparc_P371_J1081_flex_map.mrc (#29) using
1798 atoms
average map value = 0.001969, steps = 84
shifted from previous position = 3.54
rotated from previous position = 2.5 degrees
atoms outside contour = 1466, contour level = 0.003107
Position of 1oph (#27) relative to cryosparc_P371_J1081_flex_map.mrc (#29)
coordinates:
Matrix rotation and translation
0.01488540 0.98783365 0.15480023 90.39787129
0.09394517 0.15275083 -0.98378935 155.00101390
-0.99546609 0.02918683 -0.09052845 143.69933185
Axis 0.57090422 0.64827970 -0.50378746
Axis point 63.02718238 0.00000000 111.05539948
Rotation angle (degrees) 117.48046157
Shift along axis 79.69861501
> select #27/A: 195
Nothing selected
> select #27/B: 195
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 5 atom styles
> rainbow sel
> color sel red
> select add #27
1798 atoms, 1661 bonds, 397 residues, 1 model selected
> select subtract #27
Nothing selected
> select add #27
1798 atoms, 1661 bonds, 397 residues, 1 model selected
> view matrix models
> #27,0.014885,0.98783,0.1548,88.407,0.093945,0.15275,-0.98379,156.95,-0.99547,0.029187,-0.090528,145.09
> view matrix models
> #27,0.50068,0.52374,0.68922,56.841,0.53814,0.43533,-0.72173,119.4,-0.67804,0.73225,-0.063887,112.1
> view matrix models
> #27,0.50068,0.52374,0.68922,56.703,0.53814,0.43533,-0.72173,120.1,-0.67804,0.73225,-0.063887,108.86
> fitmap #27 inMap #29
Fit molecule 1oph (#27) to map cryosparc_P371_J1081_flex_map.mrc (#29) using
1798 atoms
average map value = 0.002206, steps = 72
shifted from previous position = 3.25
rotated from previous position = 11.5 degrees
atoms outside contour = 1384, contour level = 0.003107
Position of 1oph (#27) relative to cryosparc_P371_J1081_flex_map.mrc (#29)
coordinates:
Matrix rotation and translation
0.43383501 0.41278377 0.80087249 57.23345510
0.54433424 0.58824117 -0.59805732 104.34070071
-0.71797452 0.69540053 0.03050727 103.99925252
Axis 0.64695257 0.75968612 0.06579798
Axis point 48.98630646 0.00000000 62.63708921
Rotation angle (degrees) 88.49342140
Shift along axis 123.13645375
> mmaker #27 to #32
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 copy of copy of copy of 1ezx, chain C (#32) with 1oph, chain B
(#27), sequence alignment score = 997.3
RMSD between 122 pruned atom pairs is 0.798 angstroms; (across all 140 pairs:
2.232)
> hide #27 models
> show #!32 models
> hide #!31 models
> volume #29 level 0.002349
> show #27 models
> color #27 #dbd548ff
> select subtract #27
Nothing selected
> select add #27
1798 atoms, 1661 bonds, 397 residues, 1 model selected
> select subtract #27
Nothing selected
> select add #32
3984 atoms, 3982 bonds, 5 pseudobonds, 592 residues, 3 models selected
> hide #!32 models
> hide #27 models
> show #28 models
> hide #28 models
> show #27 models
> select subtract #32
Nothing selected
> select add #27
1798 atoms, 1661 bonds, 397 residues, 1 model selected
> view matrix models
> #27,-0.014536,0.98302,0.18291,86.474,0.10897,0.18339,-0.97698,152.94,-0.99394,0.00573,-0.10979,145.21
> view matrix models
> #27,-0.094668,0.98683,0.13115,91.714,0.12875,0.14277,-0.98135,154.1,-0.98715,-0.076017,-0.14057,149.8
> view matrix models
> #27,-0.094668,0.98683,0.13115,93.34,0.12875,0.14277,-0.98135,151.17,-0.98715,-0.076017,-0.14057,149.26
> view matrix models
> #27,-0.22979,0.97316,0.012679,104.9,0.38456,0.10276,-0.91736,142.04,-0.89404,-0.20593,-0.39785,168.25
> view matrix models
> #27,-0.22979,0.97316,0.012679,104.93,0.38456,0.10276,-0.91736,141.75,-0.89404,-0.20593,-0.39785,167.14
> view matrix models
> #27,-0.22979,0.97316,0.012679,104.2,0.38456,0.10276,-0.91736,144.37,-0.89404,-0.20593,-0.39785,166.13
> hide #27 models
> show #27 models
> hide #27 models
> show #27 models
> view matrix models
> #27,-0.49784,0.70316,-0.50765,154.01,0.28651,-0.41914,-0.86153,160.52,-0.81858,-0.57435,0.0072046,149.92
> view matrix models
> #27,-0.29847,0.7881,-0.53834,148.31,0.35815,-0.43034,-0.82857,156.97,-0.88467,-0.44011,-0.15381,157.66
> view matrix models
> #27,-0.24543,0.58716,-0.77137,169.05,0.40215,-0.66234,-0.63212,150.71,-0.88207,-0.46535,-0.073571,153.15
> view matrix models
> #27,-0.18594,0.44822,-0.87437,179.01,0.44471,-0.75513,-0.48167,142.87,-0.87616,-0.4784,-0.058915,152.48
> view matrix models
> #27,0.22752,0.8665,-0.44432,126.63,0.092657,-0.47348,-0.87592,168.02,-0.96935,0.15812,-0.18801,142.01
> view matrix models
> #27,0.50128,0.79078,-0.35126,116.34,0.31994,-0.54657,-0.77389,158.19,-0.80396,0.27556,-0.52699,156.35
> view matrix models
> #27,0.70079,0.62982,-0.335,115.76,0.20665,-0.62869,-0.74969,162.11,-0.68278,0.45615,-0.57073,150.23
> view matrix models
> #27,0.70079,0.62982,-0.335,118.94,0.20665,-0.62869,-0.74969,162.08,-0.68278,0.45615,-0.57073,148.91
> view matrix models
> #27,-0.4262,0.53806,-0.72722,175.4,-0.24981,-0.84263,-0.47705,162.45,-0.86946,-0.021651,0.49354,99.401
> view matrix models
> #27,-0.4262,0.53806,-0.72722,174.48,-0.24981,-0.84263,-0.47705,159.2,-0.86946,-0.021651,0.49354,98.413
> hide #27 models
> select subtract #27
Nothing selected
> hide #!29 models
> show #!30 models
> show #!29 models
> hide #!29 models
> transparency #30 50
> show #!29 models
> hide #!29 models
> volume #30 level 0.002739
> show #!24 models
> hide #!24 models
> show #!6 models
> hide #!6 models
> combine #6 close false
> select add #33
3190 atoms, 3270 bonds, 2 pseudobonds, 422 residues, 3 models selected
> view matrix models
> #33,-0.12378,0.83325,-0.53886,145.44,-0.98558,-0.040107,0.16437,137.25,0.11535,0.55143,0.8262,70.943
> view matrix models
> #33,-0.12378,0.83325,-0.53886,121.31,-0.98558,-0.040107,0.16437,137.63,0.11535,0.55143,0.8262,134.88
> view matrix models
> #33,0.096483,0.85305,0.51282,84.33,-0.9177,-0.12324,0.37767,130.03,0.38537,-0.50706,0.77096,135.66
> view matrix models
> #33,0.64301,0.74737,-0.16726,96.505,-0.76213,0.64595,-0.043654,137.8,0.075414,0.15554,0.98495,132
> view matrix models
> #33,0.64301,0.74737,-0.16726,99.153,-0.76213,0.64595,-0.043654,141.43,0.075414,0.15554,0.98495,123.21
> view matrix models
> #33,0.53757,0.81725,-0.20763,102.02,-0.84165,0.53507,-0.073018,144.14,0.051423,0.214,0.97548,123.72
> view matrix models
> #33,0.56724,0.791,-0.22925,102.27,-0.77653,0.60643,0.17101,135.07,0.2743,0.081017,0.95823,120.83
> view matrix models
> #33,0.56724,0.791,-0.22925,126.45,-0.77653,0.60643,0.17101,136.72,0.2743,0.081017,0.95823,121.23
> view matrix models
> #33,0.56724,0.791,-0.22925,77.167,-0.77653,0.60643,0.17101,133.67,0.2743,0.081017,0.95823,119.95
> view matrix models
> #33,0.74297,0.64514,-0.17831,73.008,0.66921,-0.71089,0.21633,111.62,0.012799,-0.28005,-0.9599,186.09
> view matrix models
> #33,0.09813,0.99411,-0.046082,78.903,0.94172,-0.077789,0.32727,101.1,0.32175,-0.075511,-0.94381,179.45
> view matrix models
> #33,0.09813,0.99411,-0.046082,125.57,0.94172,-0.077789,0.32727,97.242,0.32175,-0.075511,-0.94381,182.15
> view matrix models
> #33,0.09813,0.99411,-0.046082,123.79,0.94172,-0.077789,0.32727,98.857,0.32175,-0.075511,-0.94381,179.28
> view matrix models
> #33,0.09813,0.99411,-0.046082,130.36,0.94172,-0.077789,0.32727,110.04,0.32175,-0.075511,-0.94381,181.04
> view matrix models
> #33,0.18807,0.98065,-0.054404,129.09,0.97234,-0.17809,0.15115,115.39,0.13853,-0.081324,-0.98701,185.63
> view matrix models
> #33,0.12584,0.98709,-0.099091,131.56,0.99196,-0.12652,-0.00060121,119.63,-0.01313,-0.098219,-0.99508,188.6
> view matrix models
> #33,0.12584,0.98709,-0.099091,132.15,0.99196,-0.12652,-0.00060121,116.48,-0.01313,-0.098219,-0.99508,193.2
> fitmap #33 inMap #29
Fit molecule copy of 3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb (#33) to
map cryosparc_P371_J1081_flex_map.mrc (#29) using 3190 atoms
average map value = 0.003475, steps = 104
shifted from previous position = 6.47
rotated from previous position = 18.9 degrees
atoms outside contour = 969, contour level = 0.0023495
Position of copy of 3C11_Fab_D_1292144377_model-annotate_P1_HL.pdb (#33)
relative to cryosparc_P371_J1081_flex_map.mrc (#29) coordinates:
Matrix rotation and translation
-0.15475687 0.98403031 -0.08794666 131.65046804
0.97076802 0.13493018 -0.19850246 120.81278809
-0.18346579 -0.11609543 -0.97614657 191.47093637
Axis 0.64964584 0.75301343 -0.10455170
Axis point 18.09163929 0.00000000 103.49035885
Rotation angle (degrees) 176.36359820
Shift along axis 156.48121953
> select subtract #33
Nothing selected
> color #33 #dbda64ff
> show #!30 models
> hide #!29 models
> hide #!30 models
> hide #!33 models
> open /Users/apple/Downloads/cryosparc_P371_J973_003_volume_map.mrc
Opened cryosparc_P371_J973_003_volume_map.mrc as #34, grid size 300,300,300,
pixel 0.867, shown at level 0.0274, step 2, values float32
> volume #34 level 0.05742
> transparency #34 50
> show #27 models
> volume flip #34 axis z
Opened cryosparc_P371_J973_003_volume_map.mrc z flip as #35, grid size
300,300,300, pixel 0.867, shown at step 1, values float32
> select add #27
1798 atoms, 1661 bonds, 397 residues, 1 model selected
> view matrix models
> #27,-0.4262,0.53806,-0.72722,176.2,-0.24981,-0.84263,-0.47705,165.62,-0.86946,-0.021651,0.49354,102.24
> view matrix models
> #27,-0.4262,0.53806,-0.72722,178.78,-0.24981,-0.84263,-0.47705,174.86,-0.86946,-0.021651,0.49354,105.39
> view matrix models
> #27,-0.4262,0.53806,-0.72722,181.47,-0.24981,-0.84263,-0.47705,184.66,-0.86946,-0.021651,0.49354,109.78
> view matrix models
> #27,-0.4262,0.53806,-0.72722,190.87,-0.24981,-0.84263,-0.47705,217.94,-0.86946,-0.021651,0.49354,118.99
> view matrix models
> #27,-0.3858,0.47048,-0.7936,196.51,0.046117,-0.84929,-0.52592,214.13,-0.92143,-0.2395,0.30596,139.88
> view matrix models
> #27,-0.66587,0.4077,0.62482,112.13,-0.39323,0.51992,-0.75832,194.48,-0.63402,-0.75064,-0.18588,182.26
> view matrix models
> #27,-0.68529,0.37699,0.6231,113.74,-0.37744,0.54787,-0.74658,192.39,-0.62283,-0.74681,-0.23315,184.97
> view matrix models
> #27,-0.64501,-0.54498,0.53568,149.28,-0.48286,0.83399,0.26704,118.72,-0.59228,-0.086414,-0.80108,199.55
> view matrix models
> #27,-0.64501,-0.54498,0.53568,147.06,-0.48286,0.83399,0.26704,118.55,-0.59228,-0.086414,-0.80108,205.77
> view matrix models
> #27,-0.98854,-0.0066051,-0.15082,182.67,-0.13987,0.41609,0.8985,82.549,0.056821,0.9093,-0.41224,131.06
> view matrix models
> #27,-0.98854,-0.0066051,-0.15082,167.04,-0.13987,0.41609,0.8985,91.832,0.056821,0.9093,-0.41224,120.45
> view matrix models
> #27,-0.98854,-0.0066051,-0.15082,170.38,-0.13987,0.41609,0.8985,89.105,0.056821,0.9093,-0.41224,122.96
> view matrix models
> #27,-0.98854,-0.0066051,-0.15082,170.42,-0.13987,0.41609,0.8985,90.399,0.056821,0.9093,-0.41224,133.48
> volume #35 level 0.043
> open /Users/apple/Downloads/cryosparc_P371_J937_003_volume_map.mrc
Opened cryosparc_P371_J937_003_volume_map.mrc as #36, grid size 300,300,300,
pixel 0.867, shown at level 0.0245, step 2, values float32
> volume #36 level 0.06028
> hide #27 models
> select subtract #27
Nothing selected
> volume flip #36 axis z
Opened cryosparc_P371_J937_003_volume_map.mrc z flip as #37, grid size
300,300,300, pixel 0.867, shown at step 1, values float32
> transparency #37 50
> show #!31 models
> select add #31
2975 atoms, 2968 bonds, 437 residues, 1 model selected
> view matrix models
> #31,0.39135,-0.20933,0.89611,66.667,-0.16444,-0.97402,-0.15572,220.86,0.90543,-0.086415,-0.41561,82.36
> view matrix models
> #31,-0.095994,-0.17972,0.97902,91.144,-0.11035,-0.97558,-0.18991,219.49,0.98925,-0.12627,0.073818,51.003
> view matrix models
> #31,-0.095994,-0.17972,0.97902,86.989,-0.11035,-0.97558,-0.18991,196.02,0.98925,-0.12627,0.073818,43.81
> view matrix models
> #31,-0.14959,-0.29832,0.94267,99.755,-0.024842,-0.95196,-0.3052,195.83,0.98844,-0.069073,0.13499,36.818
> view matrix models
> #31,-0.14959,-0.29832,0.94267,100.18,-0.024842,-0.95196,-0.3052,202.18,0.98844,-0.069073,0.13499,38.064
> fitmap #31 inMap #37
Fit molecule copy of copy of copy of 1ezx (#31) to map
cryosparc_P371_J937_003_volume_map.mrc z flip (#37) using 2975 atoms
average map value = 0.08682, steps = 132
shifted from previous position = 2.02
rotated from previous position = 31.6 degrees
atoms outside contour = 867, contour level = 0.06028
Position of copy of copy of copy of 1ezx (#31) relative to
cryosparc_P371_J937_003_volume_map.mrc z flip (#37) coordinates:
Matrix rotation and translation
0.36233036 -0.11333577 0.92513335 57.46362679
-0.01935243 -0.99328021 -0.11410485 191.49517202
0.93184880 0.02344008 -0.36208890 68.00033796
Axis 0.82499051 -0.04027910 0.56370937
Axis point 0.00000000 96.54263836 19.29334389
Rotation angle (degrees) 175.21818737
Shift along axis 78.02612084
> mmaker #32 to #31
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 copy of copy of copy of 1ezx, chain A (#31) with copy of copy of
copy of 1ezx, chain A (#32), sequence alignment score = 1734
RMSD between 335 pruned atom pairs is 0.000 angstroms; (across all 335 pairs:
0.000)
> show #!32 models
> select subtract #31
Nothing selected
> hide #!32 models
> transparency #37 30
> transparency #37 65
> show #!32 models
> show #27 models
> mmaker #27 to #32
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 copy of copy of copy of 1ezx, chain C (#32) with 1oph, chain B
(#27), sequence alignment score = 997.3
RMSD between 122 pruned atom pairs is 0.798 angstroms; (across all 140 pairs:
2.232)
> hide #!32 models
> select #27/B: 195
5 atoms, 4 bonds, 1 residue, 1 model selected
> color sel red
> select add #27
1798 atoms, 1661 bonds, 397 residues, 1 model selected
> select subtract #27
Nothing selected
> select add #27
1798 atoms, 1661 bonds, 397 residues, 1 model selected
> view matrix models
> #27,0.0036574,-0.99591,-0.090234,167.1,0.079873,-0.089656,0.99276,103.86,-0.9968,-0.010838,0.079218,136.78
> view matrix models
> #27,0.0036574,-0.99591,-0.090234,167.32,0.079873,-0.089656,0.99276,103.5,-0.9968,-0.010838,0.079218,136.17
> view matrix models
> #27,0.0036574,-0.99591,-0.090234,167.31,0.079873,-0.089656,0.99276,103.59,-0.9968,-0.010838,0.079218,135.71
> view matrix models
> #27,-0.286,-0.74268,-0.6055,199.85,-0.56632,-0.37872,0.73202,146.21,-0.77297,0.55227,-0.31228,137.19
> view matrix models
> #27,-0.286,-0.74268,-0.6055,200.26,-0.56632,-0.37872,0.73202,145.27,-0.77297,0.55227,-0.31228,137.56
> view matrix models
> #27,-0.11735,-0.92157,-0.37006,186.61,-0.43047,-0.2886,0.85522,130.83,-0.89494,0.25966,-0.36284,153.64
> view matrix models
> #27,-0.11735,-0.92157,-0.37006,187.37,-0.43047,-0.2886,0.85522,129.56,-0.89494,0.25966,-0.36284,153.71
> fitmap #27 inMap #37
Fit molecule 1oph (#27) to map cryosparc_P371_J937_003_volume_map.mrc z flip
(#37) using 1798 atoms
average map value = 0.0548, steps = 128
shifted from previous position = 3.42
rotated from previous position = 38.8 degrees
atoms outside contour = 1047, contour level = 0.06028
Position of 1oph (#27) relative to cryosparc_P371_J937_003_volume_map.mrc z
flip (#37) coordinates:
Matrix rotation and translation
-0.45346895 -0.89029021 0.04182410 166.01007315
-0.59816316 0.33879139 0.72623772 117.01111106
-0.66073198 0.30430862 -0.68617018 166.01554475
Axis -0.48496079 0.80751043 0.33576770
Axis point 138.35331070 0.00000000 30.35915407
Rotation angle (degrees) 154.21383871
Shift along axis 69.72197468
> view matrix models
> #27,-0.92301,-0.085578,-0.37515,178.08,-0.38272,0.30509,0.87204,103.27,0.039826,0.94847,-0.31435,102.9
> view matrix models
> #27,-0.92301,-0.085578,-0.37515,178.04,-0.38272,0.30509,0.87204,107.02,0.039826,0.94847,-0.31435,104.53
> view matrix models
> #27,-0.8652,-0.36102,-0.348,184.03,-0.41726,0.13347,0.89893,111.83,-0.27809,0.92296,-0.26611,109.99
> view matrix models
> #27,-0.8652,-0.36102,-0.348,184.08,-0.41726,0.13347,0.89893,110,-0.27809,0.92296,-0.26611,108.82
> view matrix models
> #27,-0.74437,-0.58007,-0.33081,187.3,-0.42416,0.028093,0.90515,113.28,-0.51575,0.81408,-0.26695,118.33
> fitmap #27 inMap #37
Fit molecule 1oph (#27) to map cryosparc_P371_J937_003_volume_map.mrc z flip
(#37) using 1798 atoms
average map value = 0.05355, steps = 84
shifted from previous position = 0.767
rotated from previous position = 14.4 degrees
atoms outside contour = 1098, contour level = 0.06028
Position of 1oph (#27) relative to cryosparc_P371_J937_003_volume_map.mrc z
flip (#37) coordinates:
Matrix rotation and translation
-0.61577270 -0.75165872 -0.23629043 184.50519497
-0.34375795 -0.01355748 0.93896042 110.78003691
-0.70898128 0.65941290 -0.25004033 128.04401792
Axis -0.40864695 0.69098691 0.59627574
Axis point 135.45180710 0.00000000 -11.35956716
Rotation angle (degrees) 159.99876589
Shift along axis 77.49961288
> hide #!31 models
> close #34-37
> hide #27 models
> select subtract #27
Nothing selected
> save /Users/apple/Downloads/csparc.cxs includeMaps true
You deleted or moved a volume file that is still open in ChimeraX.
/Users/apple/Downloads/cryosparc_P371_J1081_noflex_map.mrc
To allow fast initial display of volume data ChimeraX does not read all data
from the file when it is first opened, and will later read more data when
needed. ChimeraX got an error trying to read the above file.
[Repeated 1 time(s)]
> close #29-30
> save /Users/apple/Downloads/csparc.cxs includeMaps true
——— End of log from Wed Dec 31 02:28:23 2025 ———
opened ChimeraX session
> open /Users/apple/Downloads/J1122.mrc
Opened J1122.mrc as #29, grid size 300,300,300, pixel 0.867, shown at level
0.0211, step 2, values float32
> volume #29 level 0.06448
> transparency #29 50
> show #!31 models
> hide #!31 models
> show #!32 models
> select add #32
3984 atoms, 3982 bonds, 5 pseudobonds, 592 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #32,-0.4387,-0.32363,-0.83834,223.29,0.093735,-0.94429,0.31548,159.1,-0.89373,0.059819,0.44459,173.61
> view matrix models
> #32,-0.051177,-0.06552,-0.99654,192.53,-0.071281,-0.99506,0.069084,187.1,-0.99614,0.074569,0.046254,202.65
> view matrix models
> #32,-0.051177,-0.06552,-0.99654,191.33,-0.071281,-0.99506,0.069084,184.14,-0.99614,0.074569,0.046254,203.41
> view matrix models
> #32,0.026039,-0.29812,-0.95417,195.35,0.13022,-0.94535,0.29892,154.62,-0.99114,-0.13204,0.014206,215.34
> view matrix models
> #32,0.026039,-0.29812,-0.95417,195.13,0.13022,-0.94535,0.29892,154.52,-0.99114,-0.13204,0.014206,218.61
> view matrix models
> #32,0.32421,-0.1599,-0.93237,166.33,0.029424,-0.98343,0.17889,170.24,-0.94553,-0.085432,-0.31413,231.84
> ui tool show "Fit in Map"
> fitmap #32 inMap #29
Fit molecule copy of copy of copy of 1ezx (#32) to map J1122.mrc (#29) using
3984 atoms
average map value = 0.08314, steps = 224
shifted from previous position = 4.3
rotated from previous position = 41.5 degrees
atoms outside contour = 1668, contour level = 0.06448
Position of copy of copy of copy of 1ezx (#32) relative to J1122.mrc (#29)
coordinates:
Matrix rotation and translation
-0.34900889 0.03003688 -0.93663792 206.58097603
0.14034902 -0.98653802 -0.08393380 177.23372304
-0.92655003 -0.16074986 0.34009489 197.98573410
Axis -0.56984891 -0.07483556 0.81833481
Axis point 168.52294892 102.29267921 0.00000000
Rotation angle (degrees) 176.13531334
Shift along axis 31.03528983
> volume #29 level 0.07099
> surface dust #29 size 8.67
> select subtract #32
Nothing selected
> open cryosparc_P371_J1130_component_001/J1130_component_001_frame_???.mrc
> vseries true
Opened map series J1130_component_001_frame_000.mrc as #30, 20 images, grid
size 300,300,300, pixel 0.867, shown at level 0.033, step 2, values float32
> volume #30.1 level 0.04835
> surface dust #29 size 8.67
> surface dust #30.1 size 8.67
> transparency #30 50
> volume #30.7 level 0.06047
> open /Users/apple/Downloads/J1134.mrc
Opened J1134.mrc as #34, grid size 300,300,300, pixel 0.867, shown at level
0.0252, step 2, values float32
> transparency #31 50
> volume #34 level 0.04544
> transparency #31450
Missing or invalid "percent" argument: Expected a number
> transparency #34 50
> hide #!32 models
> show #!34 models
> volume #34 level 0.05837
> hide #!30 models
> show #!30 models
> hide #!29 models
> show #!32 models
> show #!29 models
> hide #!34 models
> hide #!30 models
> show #!34 models
> hide #!29 models
> volume #34 level 0.0685
> mmaker #27 to #32
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 copy of copy of copy of 1ezx, chain C (#32) with 1oph, chain B
(#27), sequence alignment score = 997.3
RMSD between 122 pruned atom pairs is 0.798 angstroms; (across all 140 pairs:
2.232)
> show #27 models
> hide #!32 models
> hide #27 models
> show #!29 models
> hide #!34 models
> show #!23 models
> hide #!29 models
> show #!29 models
> show #27 models
> fitmap #27 inMap #29
Fit molecule 1oph (#27) to map J1122.mrc (#29) using 1798 atoms
average map value = 0.0518, steps = 144
shifted from previous position = 4.11
rotated from previous position = 22.4 degrees
atoms outside contour = 1430, contour level = 0.070992
Position of 1oph (#27) relative to J1122.mrc (#29) coordinates:
Matrix rotation and translation
0.02106068 0.97914469 -0.20206962 114.64292873
0.03717102 0.20120785 0.97884305 90.21390293
0.99908697 -0.02812623 -0.03215823 122.53280686
Axis -0.55065296 -0.65684271 -0.51511064
Axis point 6.14168786 0.00000000 32.08271580
Rotation angle (degrees) 113.88767131
Shift along axis -185.50276510
> select add #27
1798 atoms, 1661 bonds, 397 residues, 1 model selected
> mmaker #27 to #32
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 copy of copy of copy of 1ezx, chain C (#32) with 1oph, chain B
(#27), sequence alignment score = 997.3
RMSD between 122 pruned atom pairs is 0.798 angstroms; (across all 140 pairs:
2.232)
> view matrix models
> #27,-0.76366,-0.59209,0.2574,152.81,-0.32869,0.6997,0.63433,106.59,-0.55569,0.39981,-0.72895,190.1
> view matrix models
> #27,-0.76366,-0.59209,0.2574,153.88,-0.32869,0.6997,0.63433,107.32,-0.55569,0.39981,-0.72895,188.09
> view matrix models
> #27,-0.83313,-0.43989,0.33525,145.38,-0.083744,0.6995,0.70971,96.368,-0.54671,0.56321,-0.61961,175.22
> view matrix models
> #27,-0.74236,-0.59158,0.31452,149.59,-0.27194,0.69508,0.66552,104.03,-0.61232,0.40852,-0.67688,185.76
> view matrix models
> #27,-0.74236,-0.59158,0.31452,149.31,-0.27194,0.69508,0.66552,103.43,-0.61232,0.40852,-0.67688,186.03
> view matrix models
> #27,-0.74236,-0.59158,0.31452,149.1,-0.27194,0.69508,0.66552,103.48,-0.61232,0.40852,-0.67688,187.73
> view matrix models
> #27,-0.4433,-0.67999,0.58404,127,-0.43264,0.73295,0.52499,115.4,-0.78505,-0.019955,-0.61911,202.46
> view matrix models
> #27,-0.4433,-0.67999,0.58404,130.64,-0.43264,0.73295,0.52499,113.63,-0.78505,-0.019955,-0.61911,205.53
> fitmap #27 inMap #29
Fit molecule 1oph (#27) to map J1122.mrc (#29) using 1798 atoms
average map value = 0.05116, steps = 68
shifted from previous position = 2.69
rotated from previous position = 9.17 degrees
atoms outside contour = 1446, contour level = 0.070992
Position of 1oph (#27) relative to J1122.mrc (#29) coordinates:
Matrix rotation and translation
-0.36812181 -0.63861563 0.67576357 123.53211487
-0.32941202 0.76923775 0.54750435 107.83162875
-0.86946769 -0.02105634 -0.49354086 197.89559046
Axis -0.33937979 0.92236459 0.18456685
Axis point 134.62181234 0.00000000 42.50689250
Rotation angle (degrees) 123.10755810
Shift along axis 94.06073906
> view matrix models
> #27,0.36598,-0.2092,0.9068,76.029,-0.77877,0.46461,0.42149,137.29,-0.50949,-0.86045,0.0071194,184.16
> view matrix models
> #27,0.36598,-0.2092,0.9068,76.706,-0.77877,0.46461,0.42149,135.37,-0.50949,-0.86045,0.0071194,183.36
> fitmap #27 inMap #29
Fit molecule 1oph (#27) to map J1122.mrc (#29) using 1798 atoms
average map value = 0.05313, steps = 140
shifted from previous position = 4.46
rotated from previous position = 26.6 degrees
atoms outside contour = 1440, contour level = 0.070992
Position of 1oph (#27) relative to J1122.mrc (#29) coordinates:
Matrix rotation and translation
0.65758974 -0.02081924 0.75308850 73.16880294
-0.73687782 0.19027838 0.64869501 131.74587255
-0.15680180 -0.98150940 0.10978387 176.26543706
Axis -0.81528498 0.45504717 -0.35810958
Axis point 0.00000000 178.61895966 -24.20653672
Rotation angle (degrees) 91.21327181
Shift along axis -62.82518106
> show #!34 models
> hide #!29 models
> volume #34 level 0.07075
> close #30
> save /Users/apple/Downloads/csparc.cxs includeMaps true
——— End of log from Tue Jan 6 13:31:49 2026 ———
> view name session-start
opened ChimeraX session
> hide #!23 models
> select subtract #27
Nothing selected
> hide #27 models
> hide #!34 models
> show #!8 models
> view
> open 1oph fromDatabase pdb format mmcif
Summary of feedback from opening 1oph fetched from pdb
---
note | Fetching compressed mmCIF 1oph from http://files.rcsb.org/download/1oph.cif
1oph title:
Non-covalent complex between α-1-π-pittsburgh and S195A trypsin [more info...]
Chain information for 1oph #30
---
Chain | Description | UniProt
A | Alpha-1-antitrypsin precursor | A1AT_HUMAN 1-394
B | Trypsinogen, cationic precursor | TRY1_BOVIN -4-245
1oph mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| software_defined_assembly
> mmaker #30 to #8
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 1ezx, chain A (#8) with 1oph, chain A (#30), sequence alignment
score = 1610.1
RMSD between 212 pruned atom pairs is 0.928 angstroms; (across all 335 pairs:
9.705)
> hide #!8 models
> ui tool show "Show Sequence Viewer"
> sequence chain #30/A
Alignment identifier is 30/A
> select #30/A:21-22
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #30/A:21-83
484 atoms, 495 bonds, 63 residues, 1 model selected
> select #30/A:88
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #30/A:88-121
263 atoms, 267 bonds, 34 residues, 1 model selected
> select #30/A:121
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #30/A:105-121
127 atoms, 128 bonds, 17 residues, 1 model selected
> select #30/A:88
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #30/A:88-104
136 atoms, 138 bonds, 17 residues, 1 model selected
> select #30/A:21-45,88-104
341 atoms, 349 bonds, 42 residues, 1 model selected
> select #30/A:53
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #30/A:53-80
196 atoms, 198 bonds, 28 residues, 1 model selected
> select #30/A:21-45,53-80
401 atoms, 409 bonds, 53 residues, 1 model selected
> select #30/A:21-45,53-80,88-104
537 atoms, 547 bonds, 70 residues, 1 model selected
> select #30/A:21-45,53-80,88-104,127-137
622 atoms, 632 bonds, 81 residues, 1 model selected
> select #30/A:21-45,53-80,88-104,127-137,149-165
747 atoms, 757 bonds, 98 residues, 1 model selected
> select #30/A:21-45,53-80,88-104,127-137,149-165,199-203
783 atoms, 792 bonds, 103 residues, 1 model selected
> select #30/A:21-45,53-80,88-104,127-137,149-165,199-203,259-278
954 atoms, 965 bonds, 123 residues, 1 model selected
> select #30/A:21-45,53-80,88-104,127-137,149-165,199-203,259-278,299-306
1013 atoms, 1023 bonds, 131 residues, 1 model selected
> select
> #30/A:21-45,53-80,88-104,127-137,149-165,199-203,259-278,299-306,309-313
1053 atoms, 1063 bonds, 136 residues, 1 model selected
> select
> #30/A:21-45,53-80,88-104,127-137,149-165,199-203,259-278,299-306,309-313,349-353
1089 atoms, 1099 bonds, 141 residues, 1 model selected
> color sel hot pink
> color sel dim gray
> select clear
[Repeated 3 time(s)]
> select #30/A:112
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #30/A:112-121
71 atoms, 71 bonds, 10 residues, 1 model selected
> select #30/A:112-121,141-145
110 atoms, 110 bonds, 15 residues, 1 model selected
> select #30/A:112-121,141-145,182-191
200 atoms, 203 bonds, 25 residues, 1 model selected
> select #30/A:112-121,141-145,182-191,193-194
219 atoms, 223 bonds, 27 residues, 1 model selected
> select #30/A:112-121,141-145,182-191,193-194
219 atoms, 223 bonds, 27 residues, 1 model selected
> select #30/A:112-121,141-145,182-194
223 atoms, 228 bonds, 28 residues, 1 model selected
> select #30/A:112-121,141-145,182-194,204-211
294 atoms, 300 bonds, 36 residues, 1 model selected
> select #30/A:112-121,141-145,182-194,204-211,214
301 atoms, 306 bonds, 37 residues, 1 model selected
> select #30/A:112-121,141-145,182-194,204-211,214
301 atoms, 306 bonds, 37 residues, 1 model selected
> select #30/A:211
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #30/A:204-211
71 atoms, 72 bonds, 8 residues, 1 model selected
> select #30/A:214
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #30/A:214-232
152 atoms, 154 bonds, 19 residues, 1 model selected
> select #30/A:282
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #30/A:282-298
130 atoms, 132 bonds, 17 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #8/C #19/C #26/C #32/C
Alignment identifier is 1
> select add #30
4919 atoms, 4641 bonds, 975 residues, 1 model selected
> select subtract #30
Nothing selected
> select #30/A
3121 atoms, 2980 bonds, 578 residues, 1 model selected
> delete #30/A
> show #!8 models
> close #30
> open 1oph fromDatabase pdb format mmcif
1oph title:
Non-covalent complex between α-1-π-pittsburgh and S195A trypsin [more info...]
Chain information for 1oph #30
---
Chain | Description | UniProt
A | Alpha-1-antitrypsin precursor | A1AT_HUMAN 1-394
B | Trypsinogen, cationic precursor | TRY1_BOVIN -4-245
1oph mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| software_defined_assembly
> open 8pi2 fromDatabase pdb format mmcif
Summary of feedback from opening 8pi2 fetched from pdb
---
notes | Fetching compressed mmCIF 8pi2 from http://files.rcsb.org/download/8pi2.cif
Fetching CCD DMS from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/DMS/DMS.cif
Fetching CCD EDO from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/EDO/EDO.cif
8pi2 title:
Native alpha-1-antitrypsin at 1.5 Angstrom (Cys232Ser) [more info...]
Chain information for 8pi2 #35
---
Chain | Description | UniProt
A | Alpha-1-antitrypsin | A1AT_HUMAN 2-394
Non-standard residues in 8pi2 #35
---
DMS — dimethyl sulfoxide
EDO — 1,2-ethanediol (ethylene glycol)
GLY — glycine
203 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
2826 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> mmaker #30 to #8
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 1ezx, chain A (#8) with 1oph, chain A (#30), sequence alignment
score = 1610.1
RMSD between 212 pruned atom pairs is 0.928 angstroms; (across all 335 pairs:
9.705)
> mmaker #35 to #30
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 1oph, chain A (#30) with 8pi2, chain A (#35), sequence alignment
score = 1934.1
RMSD between 350 pruned atom pairs is 0.764 angstroms; (across all 371 pairs:
1.541)
> hide #!8 models
> hide #30 models
> show #30 models
> delete #30/A
> select add #35
5953 atoms, 5684 bonds, 699 residues, 1 model selected
> hide sel atoms
> select subtract #35
Nothing selected
> select helix
13863 atoms, 13950 bonds, 1635 residues, 21 models selected
> select add #30
15472 atoms, 15419 bonds, 2007 residues, 21 models selected
> select subtract #30
13674 atoms, 13758 bonds, 1610 residues, 20 models selected
> select add #31
15630 atoms, 15698 bonds, 1919 residues, 20 models selected
> select subtract #31
12655 atoms, 12730 bonds, 1482 residues, 19 models selected
> select add #32
15484 atoms, 15547 bonds, 5 pseudobonds, 1928 residues, 21 models selected
> select subtract #32
11500 atoms, 11565 bonds, 1336 residues, 18 models selected
> select add #33
14424 atoms, 14571 bonds, 2 pseudobonds, 1724 residues, 20 models selected
> select subtract #33
11234 atoms, 11301 bonds, 1302 residues, 17 models selected
> select add #35
15239 atoms, 15031 bonds, 1873 residues, 17 models selected
> select subtract #35
9286 atoms, 9347 bonds, 1174 residues, 16 models selected
> select add #27
10895 atoms, 10816 bonds, 1546 residues, 16 models selected
> select subtract #27
9097 atoms, 9155 bonds, 1149 residues, 15 models selected
> select add #26
11926 atoms, 11972 bonds, 5 pseudobonds, 1595 residues, 17 models selected
> select subtract #26
7942 atoms, 7990 bonds, 1003 residues, 14 models selected
> select add #25
9668 atoms, 9577 bonds, 1377 residues, 14 models selected
> select subtract #25
7785 atoms, 7832 bonds, 983 residues, 13 models selected
> select add #24
10709 atoms, 10838 bonds, 2 pseudobonds, 1371 residues, 15 models selected
> select subtract #24
7519 atoms, 7568 bonds, 949 residues, 12 models selected
> select add #23
9475 atoms, 9508 bonds, 1258 residues, 12 models selected
> select subtract #23
6500 atoms, 6540 bonds, 821 residues, 11 models selected
> select add #20
8226 atoms, 8127 bonds, 1195 residues, 11 models selected
> select subtract #20
6343 atoms, 6382 bonds, 801 residues, 10 models selected
> select add #19
9172 atoms, 9199 bonds, 5 pseudobonds, 1247 residues, 12 models selected
> select subtract #19
5188 atoms, 5217 bonds, 655 residues, 9 models selected
> select add #18
6914 atoms, 6804 bonds, 1029 residues, 9 models selected
> select subtract #18
5031 atoms, 5059 bonds, 635 residues, 8 models selected
> select add #17
7955 atoms, 8065 bonds, 2 pseudobonds, 1023 residues, 10 models selected
> select subtract #17
4765 atoms, 4795 bonds, 601 residues, 7 models selected
> select add #16
6721 atoms, 6735 bonds, 910 residues, 7 models selected
> select subtract #16
3746 atoms, 3767 bonds, 473 residues, 6 models selected
> select add #8
6575 atoms, 6584 bonds, 5 pseudobonds, 919 residues, 8 models selected
> select subtract #8
2591 atoms, 2602 bonds, 327 residues, 5 models selected
> select add #7
4317 atoms, 4189 bonds, 701 residues, 5 models selected
> select subtract #7
2434 atoms, 2444 bonds, 307 residues, 4 models selected
> select add #6
5358 atoms, 5450 bonds, 2 pseudobonds, 695 residues, 6 models selected
> select subtract #6
2168 atoms, 2180 bonds, 273 residues, 3 models selected
> select #35/A:340
19 atoms, 18 bonds, 1 residue, 1 model selected
Drag select of 11 residues
> select clear
> select #35/A:340
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #35/A:339
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #35/A:340
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #35/A:339
33 atoms, 31 bonds, 2 residues, 1 model selected
> select add #35/A:338
52 atoms, 49 bonds, 3 residues, 1 model selected
> select add #35/A:337
68 atoms, 64 bonds, 4 residues, 1 model selected
> select add #35/A:336
78 atoms, 73 bonds, 5 residues, 1 model selected
> select add #35/A:335
99 atoms, 93 bonds, 6 residues, 1 model selected
> select add #35/A:334
116 atoms, 110 bonds, 7 residues, 1 model selected
> select add #35/A:333
132 atoms, 125 bonds, 8 residues, 1 model selected
> select add #35/A:332
142 atoms, 134 bonds, 9 residues, 1 model selected
> select add #35/A:331
164 atoms, 155 bonds, 10 residues, 1 model selected
> select add #35/A:191
186 atoms, 176 bonds, 11 residues, 1 model selected
> select add #35/A:190
206 atoms, 196 bonds, 12 residues, 1 model selected
> select add #35/A:189
226 atoms, 216 bonds, 13 residues, 1 model selected
> select add #35/A:188
245 atoms, 234 bonds, 14 residues, 1 model selected
> select add #35/A:187
266 atoms, 255 bonds, 15 residues, 1 model selected
> select add #35/A:186
280 atoms, 268 bonds, 16 residues, 1 model selected
> select add #35/A:185
296 atoms, 283 bonds, 17 residues, 1 model selected
> select add #35/A:184
315 atoms, 301 bonds, 18 residues, 1 model selected
> select add #35/A:183
325 atoms, 310 bonds, 19 residues, 1 model selected
> select add #35/A:182
345 atoms, 330 bonds, 20 residues, 1 model selected
> select add #35/A:291
364 atoms, 348 bonds, 21 residues, 1 model selected
> select add #35/A:292
375 atoms, 358 bonds, 22 residues, 1 model selected
> select add #35/A:293
394 atoms, 376 bonds, 23 residues, 1 model selected
> select add #35/A:294
408 atoms, 389 bonds, 24 residues, 1 model selected
> select subtract #35/A:294
394 atoms, 376 bonds, 23 residues, 1 model selected
> select add #35/A:294
408 atoms, 389 bonds, 24 residues, 1 model selected
> select add #35/A:295
415 atoms, 395 bonds, 25 residues, 1 model selected
> select add #35/A:296
429 atoms, 408 bonds, 26 residues, 1 model selected
> select add #35/A:297
450 atoms, 429 bonds, 27 residues, 1 model selected
> select add #35/A:298
462 atoms, 440 bonds, 28 residues, 1 model selected
> select add #35/A:112
481 atoms, 458 bonds, 29 residues, 1 model selected
> select add #35/A:113
495 atoms, 471 bonds, 30 residues, 1 model selected
> select add #35/A:114
509 atoms, 484 bonds, 31 residues, 1 model selected
> select add #35/A:115
516 atoms, 490 bonds, 32 residues, 1 model selected
> select add #35/A:116
530 atoms, 503 bonds, 33 residues, 1 model selected
> select add #35/A:117
537 atoms, 509 bonds, 34 residues, 1 model selected
> select add #35/A:118
556 atoms, 527 bonds, 35 residues, 1 model selected
> select add #35/A:119
576 atoms, 547 bonds, 36 residues, 1 model selected
> select add #35/A:120
595 atoms, 565 bonds, 37 residues, 1 model selected
> select add #35/A:121
606 atoms, 575 bonds, 38 residues, 1 model selected
> select add #35/A:141
621 atoms, 589 bonds, 39 residues, 1 model selected
> select add #35/A:142
631 atoms, 598 bonds, 40 residues, 1 model selected
> select add #35/A:143
651 atoms, 618 bonds, 41 residues, 1 model selected
> select add #35/A:144
665 atoms, 631 bonds, 42 residues, 1 model selected
> select add #35/A:145
681 atoms, 646 bonds, 43 residues, 1 model selected
> color sel forest green
> color sel lime
> select clear
> select add #35/A:341
12 atoms, 11 bonds, 1 residue, 1 model selected
> select add #35/A:342
27 atoms, 25 bonds, 2 residues, 1 model selected
> select add #35/A:343
40 atoms, 37 bonds, 3 residues, 1 model selected
> select add #35/A:344
47 atoms, 43 bonds, 4 residues, 1 model selected
> select add #35/A:345
61 atoms, 56 bonds, 5 residues, 1 model selected
> select add #35/A:193
83 atoms, 77 bonds, 6 residues, 1 model selected
> select subtract #35/A:193
61 atoms, 56 bonds, 5 residues, 1 model selected
> select add #35/A:346
68 atoms, 62 bonds, 6 residues, 1 model selected
> select add #35/A:347
78 atoms, 71 bonds, 7 residues, 1 model selected
> select add #35/A:348
88 atoms, 80 bonds, 8 residues, 1 model selected
> select add #35/A:349
95 atoms, 86 bonds, 9 residues, 1 model selected
> select add #35/A:350
105 atoms, 95 bonds, 10 residues, 1 model selected
> select add #35/A:351
112 atoms, 101 bonds, 11 residues, 1 model selected
> select add #35/A:352
132 atoms, 121 bonds, 12 residues, 1 model selected
> select add #35/A:353
151 atoms, 139 bonds, 13 residues, 1 model selected
> select add #35/A:354
166 atoms, 153 bonds, 14 residues, 1 model selected
> select add #35/A:355
176 atoms, 162 bonds, 15 residues, 1 model selected
> select add #35/A:356
195 atoms, 180 bonds, 16 residues, 1 model selected
> select add #35/A:357
209 atoms, 194 bonds, 17 residues, 1 model selected
> select add #35/A:358
226 atoms, 210 bonds, 18 residues, 1 model selected
> select add #35/A:359
237 atoms, 220 bonds, 19 residues, 1 model selected
> select add #35/A:360
256 atoms, 238 bonds, 20 residues, 1 model selected
> select add #35/A:361
270 atoms, 252 bonds, 21 residues, 1 model selected
> select add #35/A:362
284 atoms, 266 bonds, 22 residues, 1 model selected
> select add #35/A:363
299 atoms, 280 bonds, 23 residues, 1 model selected
> select subtract #35/A:363
284 atoms, 266 bonds, 22 residues, 1 model selected
> color sel red
> select clear
> select add #35/A:363
15 atoms, 14 bonds, 1 residue, 1 model selected
> select add #35/A:364
31 atoms, 29 bonds, 2 residues, 1 model selected
> select add #35/A:365
53 atoms, 50 bonds, 3 residues, 1 model selected
> select add #35/A:282
77 atoms, 73 bonds, 4 residues, 1 model selected
> select add #35/A:283
88 atoms, 83 bonds, 5 residues, 1 model selected
> select add #35/A:284
98 atoms, 92 bonds, 6 residues, 1 model selected
> select add #35/A:285
109 atoms, 102 bonds, 7 residues, 1 model selected
> select add #35/A:286
128 atoms, 120 bonds, 8 residues, 1 model selected
> select add #35/A:287
146 atoms, 138 bonds, 9 residues, 1 model selected
> select add #35/A:288
165 atoms, 156 bonds, 10 residues, 1 model selected
> select add #35/A:289
179 atoms, 170 bonds, 11 residues, 1 model selected
> select add #35/A:224
198 atoms, 188 bonds, 12 residues, 1 model selected
> select add #35/A:223
222 atoms, 211 bonds, 13 residues, 1 model selected
> select add #35/A:222
244 atoms, 232 bonds, 14 residues, 1 model selected
> select add #35/A:221
261 atoms, 248 bonds, 15 residues, 1 model selected
> select add #35/A:220
278 atoms, 264 bonds, 16 residues, 1 model selected
> select add #35/A:219
292 atoms, 278 bonds, 17 residues, 1 model selected
> select add #35/A:218
308 atoms, 293 bonds, 18 residues, 1 model selected
> select add #35/A:217
330 atoms, 314 bonds, 19 residues, 1 model selected
> select add #35/A:216
346 atoms, 329 bonds, 20 residues, 1 model selected
> select add #35/A:215
360 atoms, 342 bonds, 21 residues, 1 model selected
> select add #35/A:214
374 atoms, 355 bonds, 22 residues, 1 model selected
> select add #35/A:204
389 atoms, 369 bonds, 23 residues, 1 model selected
> select add #35/A:205
404 atoms, 383 bonds, 24 residues, 1 model selected
> select add #35/A:206
419 atoms, 397 bonds, 25 residues, 1 model selected
> select subtract #35/A:206
404 atoms, 383 bonds, 24 residues, 1 model selected
> select add #35/A:207
416 atoms, 394 bonds, 25 residues, 1 model selected
> select add #35/A:206
431 atoms, 408 bonds, 26 residues, 1 model selected
> select add #35/A:208
451 atoms, 428 bonds, 27 residues, 1 model selected
> select add #35/A:209
468 atoms, 445 bonds, 28 residues, 1 model selected
> select add #35/A:210
484 atoms, 460 bonds, 29 residues, 1 model selected
> select add #35/A:211
496 atoms, 471 bonds, 30 residues, 1 model selected
> color sel light sea green
> color sel blue
> color sel cornflower blue
> select clear
> select add #35/A:228
14 atoms, 13 bonds, 1 residue, 1 model selected
> select add #35/A:229
33 atoms, 31 bonds, 2 residues, 1 model selected
> select add #35/A:230
50 atoms, 47 bonds, 3 residues, 1 model selected
> select add #35/A:231
67 atoms, 64 bonds, 4 residues, 1 model selected
> select add #35/A:232
78 atoms, 74 bonds, 5 residues, 1 model selected
> select add #35/A:237
89 atoms, 84 bonds, 6 residues, 1 model selected
> select add #35/A:238
113 atoms, 109 bonds, 7 residues, 1 model selected
> select add #35/A:239
129 atoms, 124 bonds, 8 residues, 1 model selected
> select add #35/A:240
148 atoms, 142 bonds, 9 residues, 1 model selected
> select add #35/A:241
167 atoms, 160 bonds, 10 residues, 1 model selected
> select add #35/A:242
184 atoms, 176 bonds, 11 residues, 1 model selected
> select add #35/A:243
200 atoms, 191 bonds, 12 residues, 1 model selected
> select add #35/A:244
221 atoms, 212 bonds, 13 residues, 1 model selected
> select add #35/A:248
231 atoms, 221 bonds, 14 residues, 1 model selected
> select add #35/A:249
245 atoms, 234 bonds, 15 residues, 1 model selected
> select add #35/A:250
255 atoms, 243 bonds, 16 residues, 1 model selected
> select add #35/A:251
274 atoms, 261 bonds, 17 residues, 1 model selected
> select add #35/A:252
294 atoms, 281 bonds, 18 residues, 1 model selected
> select add #35/A:253
314 atoms, 301 bonds, 19 residues, 1 model selected
> select add #35/A:254
333 atoms, 319 bonds, 20 residues, 1 model selected
> select add #35/A:255
347 atoms, 333 bonds, 21 residues, 1 model selected
> select add #35/A:247
361 atoms, 346 bonds, 22 residues, 1 model selected
> select add #35/A:246
368 atoms, 352 bonds, 23 residues, 1 model selected
> select add #35/A:245
387 atoms, 370 bonds, 24 residues, 1 model selected
> select add #35/A:376
402 atoms, 384 bonds, 25 residues, 1 model selected
> select add #35/A:375
421 atoms, 402 bonds, 26 residues, 1 model selected
> select add #35/A:374
438 atoms, 418 bonds, 27 residues, 1 model selected
> select add #35/A:373
457 atoms, 436 bonds, 28 residues, 1 model selected
> select add #35/A:372
477 atoms, 456 bonds, 29 residues, 1 model selected
> select add #35/A:371
493 atoms, 471 bonds, 30 residues, 1 model selected
> select add #35/A:370
513 atoms, 491 bonds, 31 residues, 1 model selected
> select add #35/A:388
529 atoms, 506 bonds, 32 residues, 1 model selected
> select add #35/A:387
551 atoms, 527 bonds, 33 residues, 1 model selected
> select add #35/A:386
558 atoms, 533 bonds, 34 residues, 1 model selected
> select add #35/A:385
575 atoms, 549 bonds, 35 residues, 1 model selected
> select add #35/A:384
595 atoms, 569 bonds, 36 residues, 1 model selected
> select add #35/A:383
614 atoms, 587 bonds, 37 residues, 1 model selected
> select add #35/A:382
628 atoms, 601 bonds, 38 residues, 1 model selected
> select add #35/A:50
647 atoms, 619 bonds, 39 residues, 1 model selected
> select add #35/A:51
667 atoms, 639 bonds, 40 residues, 1 model selected
> select add #35/A:52
687 atoms, 659 bonds, 41 residues, 1 model selected
> select add #35/A:227
707 atoms, 679 bonds, 42 residues, 1 model selected
> color sel yellow
> select clear
> select add #35/A:225
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel cornflower blue
> select clear
> select add #35/A:226
17 atoms, 16 bonds, 1 residue, 1 model selected
> color sel cornflower blue
> select clear
[Repeated 1 time(s)]
> select add #35/A:165
14 atoms, 13 bonds, 1 residue, 1 model selected
> select add #35/A:163
27 atoms, 25 bonds, 2 residues, 1 model selected
> select add #35/A:162
42 atoms, 39 bonds, 3 residues, 1 model selected
> select add #35/A:164
49 atoms, 45 bonds, 4 residues, 1 model selected
> select add #35/A:161
65 atoms, 60 bonds, 5 residues, 1 model selected
> select add #35/A:160
86 atoms, 81 bonds, 6 residues, 1 model selected
> select add #35/A:159
98 atoms, 92 bonds, 7 residues, 1 model selected
> select add #35/A:158
112 atoms, 105 bonds, 8 residues, 1 model selected
> select add #35/A:157
131 atoms, 123 bonds, 9 residues, 1 model selected
> select add #35/A:155
153 atoms, 144 bonds, 10 residues, 1 model selected
> select add #35/A:156
170 atoms, 160 bonds, 11 residues, 1 model selected
> select add #35/A:154
192 atoms, 181 bonds, 12 residues, 1 model selected
> select add #35/A:153
202 atoms, 190 bonds, 13 residues, 1 model selected
> select add #35/A:152
217 atoms, 204 bonds, 14 residues, 1 model selected
> select add #35/A:151
232 atoms, 218 bonds, 15 residues, 1 model selected
> select add #35/A:150
246 atoms, 231 bonds, 16 residues, 1 model selected
> select add #35/A:149
258 atoms, 242 bonds, 17 residues, 1 model selected
> select add #35/A:336
268 atoms, 251 bonds, 18 residues, 1 model selected
> select subtract #35/A:336
258 atoms, 242 bonds, 17 residues, 1 model selected
> select add #35/A:166
275 atoms, 258 bonds, 18 residues, 1 model selected
> select add #35/A:167
282 atoms, 264 bonds, 19 residues, 1 model selected
> select add #35/A:168
292 atoms, 273 bonds, 20 residues, 1 model selected
> select add #35/A:169
311 atoms, 291 bonds, 21 residues, 1 model selected
> select add #35/A:170
327 atoms, 306 bonds, 22 residues, 1 model selected
> select add #35/A:171
339 atoms, 317 bonds, 23 residues, 1 model selected
> select add #35/A:172
358 atoms, 335 bonds, 24 residues, 1 model selected
> select add #35/A:173
374 atoms, 350 bonds, 25 residues, 1 model selected
> select add #35/A:174
396 atoms, 371 bonds, 26 residues, 1 model selected
> select add #35/A:175
406 atoms, 380 bonds, 27 residues, 1 model selected
> select add #35/A:176
425 atoms, 398 bonds, 28 residues, 1 model selected
> select add #35/A:177
432 atoms, 404 bonds, 29 residues, 1 model selected
> select add #35/A:178
439 atoms, 410 bonds, 30 residues, 1 model selected
> select add #35/A:179
446 atoms, 416 bonds, 31 residues, 1 model selected
> select add #35/A:180
460 atoms, 429 bonds, 32 residues, 1 model selected
> select add #35/A:181
476 atoms, 444 bonds, 33 residues, 1 model selected
> select add #35
5953 atoms, 5684 bonds, 699 residues, 1 model selected
> select subtract #35
Nothing selected
> color #35 #bbb0abff
> color #35 #bbb8b6ff
> select add #35/A:340
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #35/A:339
33 atoms, 31 bonds, 2 residues, 1 model selected
> select add #35/A:338
52 atoms, 49 bonds, 3 residues, 1 model selected
> select add #35/A:337
68 atoms, 64 bonds, 4 residues, 1 model selected
> select add #35/A:336
78 atoms, 73 bonds, 5 residues, 1 model selected
> select add #35/A:335
99 atoms, 93 bonds, 6 residues, 1 model selected
> select add #35/A:334
116 atoms, 110 bonds, 7 residues, 1 model selected
> select add #35/A:333
132 atoms, 125 bonds, 8 residues, 1 model selected
> select add #35/A:332
142 atoms, 134 bonds, 9 residues, 1 model selected
> select add #35/A:331
164 atoms, 155 bonds, 10 residues, 1 model selected
> select add #35/A:291
183 atoms, 173 bonds, 11 residues, 1 model selected
> select add #35/A:292
194 atoms, 183 bonds, 12 residues, 1 model selected
> select add #35/A:293
213 atoms, 201 bonds, 13 residues, 1 model selected
> select add #35/A:294
227 atoms, 214 bonds, 14 residues, 1 model selected
> select add #35/A:295
234 atoms, 220 bonds, 15 residues, 1 model selected
> select add #35/A:296
248 atoms, 233 bonds, 16 residues, 1 model selected
> select add #35/A:297
269 atoms, 254 bonds, 17 residues, 1 model selected
> select add #35/A:298
281 atoms, 265 bonds, 18 residues, 1 model selected
> select add #35/A:191
303 atoms, 286 bonds, 19 residues, 1 model selected
> select add #35/A:190
323 atoms, 306 bonds, 20 residues, 1 model selected
> select add #35/A:189
343 atoms, 326 bonds, 21 residues, 1 model selected
> select add #35/A:188
362 atoms, 344 bonds, 22 residues, 1 model selected
> select add #35/A:187
383 atoms, 365 bonds, 23 residues, 1 model selected
> select add #35/A:186
397 atoms, 378 bonds, 24 residues, 1 model selected
> select add #35/A:185
413 atoms, 393 bonds, 25 residues, 1 model selected
> select add #35/A:184
432 atoms, 411 bonds, 26 residues, 1 model selected
> select add #35/A:183
442 atoms, 420 bonds, 27 residues, 1 model selected
> select add #35/A:182
462 atoms, 440 bonds, 28 residues, 1 model selected
> select add #35/A:121
473 atoms, 450 bonds, 29 residues, 1 model selected
> select add #35/A:120
492 atoms, 468 bonds, 30 residues, 1 model selected
> select add #35/A:119
512 atoms, 488 bonds, 31 residues, 1 model selected
> select add #35/A:118
531 atoms, 506 bonds, 32 residues, 1 model selected
> select add #35/A:117
538 atoms, 512 bonds, 33 residues, 1 model selected
> select add #35/A:116
552 atoms, 525 bonds, 34 residues, 1 model selected
> select add #35/A:115
559 atoms, 531 bonds, 35 residues, 1 model selected
> select add #35/A:114
573 atoms, 544 bonds, 36 residues, 1 model selected
> select add #35/A:113
587 atoms, 557 bonds, 37 residues, 1 model selected
> select add #35/A:112
606 atoms, 575 bonds, 38 residues, 1 model selected
> select add #35/A:141
621 atoms, 589 bonds, 39 residues, 1 model selected
> select add #35/A:142
631 atoms, 598 bonds, 40 residues, 1 model selected
> select add #35/A:143
651 atoms, 618 bonds, 41 residues, 1 model selected
> select add #35/A:144
665 atoms, 631 bonds, 42 residues, 1 model selected
> select add #35/A:145
681 atoms, 646 bonds, 43 residues, 1 model selected
> color sel light sea green
> color sel lime
> select clear
> select add #35/A:341
12 atoms, 11 bonds, 1 residue, 1 model selected
> select add #35/A:342
27 atoms, 25 bonds, 2 residues, 1 model selected
> select add #35/A:343
40 atoms, 37 bonds, 3 residues, 1 model selected
> select add #35/A:344
47 atoms, 43 bonds, 4 residues, 1 model selected
> select add #35/A:345
61 atoms, 56 bonds, 5 residues, 1 model selected
> select add #35/A:346
68 atoms, 62 bonds, 6 residues, 1 model selected
> select add #35/A:347
78 atoms, 71 bonds, 7 residues, 1 model selected
> select add #35/A:348
88 atoms, 80 bonds, 8 residues, 1 model selected
> select add #35/A:349
95 atoms, 86 bonds, 9 residues, 1 model selected
> select add #35/A:350
105 atoms, 95 bonds, 10 residues, 1 model selected
> select add #35/A:351
112 atoms, 101 bonds, 11 residues, 1 model selected
> select add #35/A:352
132 atoms, 121 bonds, 12 residues, 1 model selected
> select add #35/A:353
151 atoms, 139 bonds, 13 residues, 1 model selected
> select add #35/A:354
166 atoms, 153 bonds, 14 residues, 1 model selected
> select add #35/A:355
176 atoms, 162 bonds, 15 residues, 1 model selected
> select add #35/A:356
195 atoms, 180 bonds, 16 residues, 1 model selected
> select add #35/A:357
209 atoms, 194 bonds, 17 residues, 1 model selected
> select add #35/A:358
226 atoms, 210 bonds, 18 residues, 1 model selected
> select add #35/A:359
237 atoms, 220 bonds, 19 residues, 1 model selected
> select add #35/A:360
256 atoms, 238 bonds, 20 residues, 1 model selected
> select add #35/A:361
270 atoms, 252 bonds, 21 residues, 1 model selected
> select add #35/A:362
284 atoms, 266 bonds, 22 residues, 1 model selected
> color sel red
> select clear
> select add #35/A:165
14 atoms, 13 bonds, 1 residue, 1 model selected
> select add #35/A:164
21 atoms, 19 bonds, 2 residues, 1 model selected
> select add #35/A:163
34 atoms, 31 bonds, 3 residues, 1 model selected
> select add #35/A:162
49 atoms, 45 bonds, 4 residues, 1 model selected
> select add #35/A:161
65 atoms, 60 bonds, 5 residues, 1 model selected
> select add #35/A:160
86 atoms, 81 bonds, 6 residues, 1 model selected
> select add #35/A:159
98 atoms, 92 bonds, 7 residues, 1 model selected
> select add #35/A:158
112 atoms, 105 bonds, 8 residues, 1 model selected
> select add #35/A:157
131 atoms, 123 bonds, 9 residues, 1 model selected
> select add #35/A:156
148 atoms, 139 bonds, 10 residues, 1 model selected
> select add #35/A:155
170 atoms, 160 bonds, 11 residues, 1 model selected
> select add #35/A:154
192 atoms, 181 bonds, 12 residues, 1 model selected
> select add #35/A:153
202 atoms, 190 bonds, 13 residues, 1 model selected
> select add #35/A:152
217 atoms, 204 bonds, 14 residues, 1 model selected
> select add #35/A:151
232 atoms, 218 bonds, 15 residues, 1 model selected
> select add #35/A:150
246 atoms, 231 bonds, 16 residues, 1 model selected
> select add #35/A:149
258 atoms, 242 bonds, 17 residues, 1 model selected
> color sel magenta
> select clear
[Repeated 1 time(s)]
> color #30 #bcc7ceff
> color #30 #67c7ceff
> color #30 #0cc5ceff
> color #30 #07ce85ff
> color #30 #10ccceff
> color #30 #016fceff
> select #30/B:195
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> swapp S
Unknown command: swapp S
> delete #30/A swapaa S
Expected a keyword
> swapaa #30/B:195 ser
Using Dunbrack library
1oph #30/B ALA 195: phi -47.1, psi 140.5 trans
Density criteria with multiple volume models open;
Need to specify one to use via 'density' keyword.
> ui tool show Rotamers
Populating font family aliases took 55 ms. Replace uses of missing font family
"Times" with one that exists to avoid this cost.
> select #30/B:195
5 atoms, 4 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel SER rotLib Dunbrack
1oph #30/B ALA 195: phi -47.1, psi 140.5 trans
Changed 9 bond radii
No rotamers selected. Click the 'Calculate' button (not 'OK') to add a column
to the table.
> undo
[Repeated 2 time(s)]
> ui tool show Rotamers
> swapaa interactive sel SER rotLib Dunbrack
1oph #!30/B ALA 195: phi -47.1, psi 140.5 trans
Changed 9 bond radii
> swapaa #!30/B:195 SER criteria 3 rotLib Dunbrack
Using Dunbrack library
1oph #!30/B ALA 195: phi -47.1, psi 140.5 trans
Applying SER rotamer (chi angles: 64.0) to 1oph #!30/B SER 195
> hide sel atoms
[Repeated 2 time(s)]
> select #30/B:195
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #30/B:195
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> select clear
> select #30.1.1/A:1@CB
1 atom, 1 residue, 1 model selected
> swapaa #!30/B:195 SER criteria 2 rotLib Dunbrack
Using Dunbrack library
1oph #!30/B SER 195: phi -47.1, psi 140.5 trans
Applying SER rotamer (chi angles: -63.9) to 1oph #!30/B SER 195
> select #30/B:195
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> rainbow sel
> select clear
> select #35/A:358
17 atoms, 16 bonds, 1 residue, 1 model selected
> show sel atoms
> rainbow sel
[Repeated 1 time(s)]
> color sel byhetero
> color sel red
> color sel byhetero
> select clear
> open 1oph fromDatabase pdb format mmcif
1oph title:
Non-covalent complex between α-1-π-pittsburgh and S195A trypsin [more info...]
Chain information for 1oph #36
---
Chain | Description | UniProt
A | Alpha-1-antitrypsin precursor | A1AT_HUMAN 1-394
B | Trypsinogen, cationic precursor | TRY1_BOVIN -4-245
1oph mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| software_defined_assembly
> mmaker #36 to #35
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 8pi2, chain A (#35) with 1oph, chain A (#36), sequence alignment
score = 1934.1
RMSD between 350 pruned atom pairs is 0.764 angstroms; (across all 371 pairs:
1.541)
> select #36/A
3121 atoms, 2980 bonds, 578 residues, 1 model selected
> select #36/A: 358
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> hide #30 models
> show #30 models
> style sel stick
Changed 11 atom styles
> style sel ball
Changed 11 atom styles
> style sel stick
Changed 11 atom styles
> hide #35 models
> show #35 models
> select #36/A: 57
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #36
4919 atoms, 4641 bonds, 975 residues, 1 model selected
> select subtract #36
Nothing selected
> hide #36 models
> select #30/A: 57
Nothing selected
> select #30/B: 57
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select #30/B: 202
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #30/B: 102
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select #30/B: 194
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> select add #30
1799 atoms, 1662 bonds, 397 residues, 1 model selected
> hide sel atoms
> select add #35
7752 atoms, 7346 bonds, 1096 residues, 2 models selected
> hide sel atoms
> select subtract #30
5953 atoms, 5684 bonds, 699 residues, 1 model selected
> select subtract #35
Nothing selected
> show #!8 models
> open 1ezx fromDatabase pdb format mmcif
Summary of feedback from opening 1ezx fetched from pdb
---
note | Fetching compressed mmCIF 1ezx from http://files.rcsb.org/download/1ezx.cif
1ezx title:
Crystal structure of A serpin:protease complex [more info...]
Chain information for 1ezx #37
---
Chain | Description | UniProt
A | ALPHA-1-ANTITRYPSIN | A1AT_HUMAN 24-358
B | ALPHA-1-ANTITRYPSIN | A1AT_HUMAN 359-394
C | TRYPSIN | TRY1_BOVIN 42-245
> mmaker #37 to #35
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 8pi2, chain A (#35) with 1ezx, chain A (#37), sequence alignment
score = 1629.2
RMSD between 219 pruned atom pairs is 0.866 angstroms; (across all 335 pairs:
9.271)
> hide #!8 models
> hide #30 models
> hide #35 models
> select #37/A
2686 atoms, 2674 bonds, 398 residues, 1 model selected
> select #37/A,B
2975 atoms, 2968 bonds, 437 residues, 1 model selected
> color sel dark gray
> select clear
> show #35 models
> hide #!37 models
> show #!37 models
> hide #35 models
> show #35 models
> hide #35 models
> select #37/C
1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 2 models selected
> show #30 models
> color (#!37 & sel) cornflower blue
> color (#!37 & sel) blue
> select clear
> select #37/C
1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 2 models selected
> color (#!37 & sel) cornflower blue
> select clear
> select #37/C
1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 2 models selected
> color (#!37 & sel) medium blue
> color (#!37 & sel) cornflower blue
> select 30
Expected an objects specifier or a keyword
> select 30/B
Expected an objects specifier or a keyword
> select 30/A
Expected an objects specifier or a keyword
> select #30
1799 atoms, 1662 bonds, 397 residues, 1 model selected
> color sel cornflower blue
> select clear
> select #37/A:291
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #37/A:292
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #37/A:291
14 atoms, 12 bonds, 2 residues, 1 model selected
> select add #37/A:293
22 atoms, 19 bonds, 3 residues, 1 model selected
> select add #37/A:294
29 atoms, 25 bonds, 4 residues, 1 model selected
> select add #37/A:295
33 atoms, 28 bonds, 5 residues, 1 model selected
> select add #37/A:296
40 atoms, 34 bonds, 6 residues, 1 model selected
> select add #37/A:297
52 atoms, 46 bonds, 7 residues, 1 model selected
> select add #37/A:298
60 atoms, 53 bonds, 8 residues, 1 model selected
> select add #37/A:340
68 atoms, 60 bonds, 9 residues, 1 model selected
> select add #37/A:339
75 atoms, 66 bonds, 10 residues, 1 model selected
> select add #37/A:338
83 atoms, 73 bonds, 11 residues, 1 model selected
> select add #37/A:337
90 atoms, 79 bonds, 12 residues, 1 model selected
> select add #37/A:336
95 atoms, 83 bonds, 13 residues, 1 model selected
> select add #37/A:335
104 atoms, 91 bonds, 14 residues, 1 model selected
> select add #37/A:334
114 atoms, 101 bonds, 15 residues, 1 model selected
> select add #37/A:333
121 atoms, 107 bonds, 16 residues, 1 model selected
> select add #37/A:332
126 atoms, 111 bonds, 17 residues, 1 model selected
> select add #37/A:331
135 atoms, 119 bonds, 18 residues, 1 model selected
> select add #37/A:330
141 atoms, 124 bonds, 19 residues, 1 model selected
> select add #37/A:329
149 atoms, 131 bonds, 20 residues, 1 model selected
> select add #37/A:328
158 atoms, 139 bonds, 21 residues, 1 model selected
> select add #37/A:327
166 atoms, 146 bonds, 22 residues, 1 model selected
> select add #37/A:357
173 atoms, 153 bonds, 23 residues, 1 model selected
> select add #37/A:356
181 atoms, 160 bonds, 24 residues, 1 model selected
> select add #37/A:355
186 atoms, 164 bonds, 25 residues, 1 model selected
> select add #37/A:354
195 atoms, 172 bonds, 26 residues, 1 model selected
> select add #37/A:353
203 atoms, 179 bonds, 27 residues, 1 model selected
> select add #37/A:352
214 atoms, 190 bonds, 28 residues, 1 model selected
> select add #37/A:351
222 atoms, 197 bonds, 29 residues, 1 model selected
> select add #37/A:350
227 atoms, 201 bonds, 30 residues, 1 model selected
> select add #37/A:349
231 atoms, 204 bonds, 31 residues, 1 model selected
> select add #37/A:348
236 atoms, 208 bonds, 32 residues, 1 model selected
> select add #37/A:347
241 atoms, 212 bonds, 33 residues, 1 model selected
> select add #37/A:346
250 atoms, 220 bonds, 34 residues, 1 model selected
> select add #37/A:345
257 atoms, 226 bonds, 35 residues, 1 model selected
> select add #37/A:344
261 atoms, 229 bonds, 36 residues, 1 model selected
> select add #37/A:193
270 atoms, 237 bonds, 37 residues, 1 model selected
> select add #37/A:192
274 atoms, 240 bonds, 38 residues, 1 model selected
> select add #37/A:191
283 atoms, 248 bonds, 39 residues, 1 model selected
> select add #37/A:190
294 atoms, 259 bonds, 40 residues, 1 model selected
> select add #37/A:189
305 atoms, 270 bonds, 41 residues, 1 model selected
> select add #37/A:188
313 atoms, 277 bonds, 42 residues, 1 model selected
> select add #37/A:187
325 atoms, 289 bonds, 43 residues, 1 model selected
> select add #37/A:186
333 atoms, 296 bonds, 44 residues, 1 model selected
> select add #37/A:185
340 atoms, 302 bonds, 45 residues, 1 model selected
> select add #37/A:184
348 atoms, 309 bonds, 46 residues, 1 model selected
> select add #37/A:183
353 atoms, 313 bonds, 47 residues, 1 model selected
> select add #37/A:182
364 atoms, 324 bonds, 48 residues, 1 model selected
> select subtract #37/A:182
353 atoms, 313 bonds, 47 residues, 1 model selected
> select subtract #37/A:183
348 atoms, 309 bonds, 46 residues, 1 model selected
> select subtract #37/A:184
340 atoms, 302 bonds, 45 residues, 1 model selected
> select subtract #37/A:185
333 atoms, 296 bonds, 44 residues, 1 model selected
> select subtract #37/A:186
325 atoms, 289 bonds, 43 residues, 1 model selected
> select subtract #37/A:187
313 atoms, 277 bonds, 42 residues, 1 model selected
> select subtract #37/A:188
305 atoms, 270 bonds, 41 residues, 1 model selected
> select subtract #37/A:189
294 atoms, 259 bonds, 40 residues, 1 model selected
> select subtract #37/A:190
283 atoms, 248 bonds, 39 residues, 1 model selected
> select subtract #37/A:191
274 atoms, 240 bonds, 38 residues, 1 model selected
> select subtract #37/A:192
270 atoms, 237 bonds, 37 residues, 1 model selected
> select subtract #37/A:193
261 atoms, 229 bonds, 36 residues, 1 model selected
> select subtract #37/A:357
254 atoms, 222 bonds, 35 residues, 1 model selected
> select subtract #37/A:356
246 atoms, 215 bonds, 34 residues, 1 model selected
> select subtract #37/A:355
241 atoms, 211 bonds, 33 residues, 1 model selected
> select subtract #37/A:354
232 atoms, 203 bonds, 32 residues, 1 model selected
> select subtract #37/A:353
224 atoms, 196 bonds, 31 residues, 1 model selected
> select subtract #37/A:352
213 atoms, 185 bonds, 30 residues, 1 model selected
> select subtract #37/A:351
205 atoms, 178 bonds, 29 residues, 1 model selected
> select subtract #37/A:350
200 atoms, 174 bonds, 28 residues, 1 model selected
> select subtract #37/A:349
196 atoms, 171 bonds, 27 residues, 1 model selected
> select subtract #37/A:348
191 atoms, 167 bonds, 26 residues, 1 model selected
> select subtract #37/A:347
186 atoms, 163 bonds, 25 residues, 1 model selected
> select subtract #37/A:346
177 atoms, 155 bonds, 24 residues, 1 model selected
> select subtract #37/A:345
170 atoms, 149 bonds, 23 residues, 1 model selected
> select subtract #37/A:344
166 atoms, 146 bonds, 22 residues, 1 model selected
> select add #37/A:193
175 atoms, 154 bonds, 23 residues, 1 model selected
> select add #37/A:192
179 atoms, 157 bonds, 24 residues, 1 model selected
> select add #37/A:191
188 atoms, 165 bonds, 25 residues, 1 model selected
> select add #37/A:190
199 atoms, 176 bonds, 26 residues, 1 model selected
> select add #37/A:189
210 atoms, 187 bonds, 27 residues, 1 model selected
> select add #37/A:188
218 atoms, 194 bonds, 28 residues, 1 model selected
> select add #37/A:187
230 atoms, 206 bonds, 29 residues, 1 model selected
> select add #37/A:186
238 atoms, 213 bonds, 30 residues, 1 model selected
> select add #37/A:185
245 atoms, 219 bonds, 31 residues, 1 model selected
> select add #37/A:184
253 atoms, 226 bonds, 32 residues, 1 model selected
> select add #37/A:183
258 atoms, 230 bonds, 33 residues, 1 model selected
> select add #37/A:182
269 atoms, 241 bonds, 34 residues, 1 model selected
> select add #37/A:111
278 atoms, 249 bonds, 35 residues, 1 model selected
> select add #37/A:112
286 atoms, 256 bonds, 36 residues, 1 model selected
> select subtract #37/A:112
278 atoms, 249 bonds, 35 residues, 1 model selected
> select add #37/A:112
286 atoms, 256 bonds, 36 residues, 1 model selected
> select add #37/A:113
293 atoms, 262 bonds, 37 residues, 1 model selected
> select add #37/A:114
300 atoms, 268 bonds, 38 residues, 1 model selected
> select add #37/A:115
304 atoms, 271 bonds, 39 residues, 1 model selected
> select add #37/A:116
312 atoms, 278 bonds, 40 residues, 1 model selected
> select add #37/A:117
316 atoms, 281 bonds, 41 residues, 1 model selected
> select add #37/A:118
324 atoms, 288 bonds, 42 residues, 1 model selected
> select subtract #37/A:118
316 atoms, 281 bonds, 41 residues, 1 model selected
> select add #37/A:119
327 atoms, 292 bonds, 42 residues, 1 model selected
> select add #37/A:118
335 atoms, 299 bonds, 43 residues, 1 model selected
> select add #37/A:120
343 atoms, 306 bonds, 44 residues, 1 model selected
> select add #37/A:121
349 atoms, 311 bonds, 45 residues, 1 model selected
> select add #37/A:145
356 atoms, 317 bonds, 46 residues, 1 model selected
> select add #37/A:144
363 atoms, 323 bonds, 47 residues, 1 model selected
> select add #37/A:143
374 atoms, 334 bonds, 48 residues, 1 model selected
> select add #37/A:142
379 atoms, 338 bonds, 49 residues, 1 model selected
> select add #37/A:141
388 atoms, 346 bonds, 50 residues, 1 model selected
> color sel cyan
> color sel forest green
> color sel lime
> select clear
> select add #37/A:358
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #37/A:357
15 atoms, 14 bonds, 2 residues, 1 model selected
> select add #37/A:356
23 atoms, 21 bonds, 3 residues, 1 model selected
> select add #37/A:355
28 atoms, 25 bonds, 4 residues, 1 model selected
> select add #37/A:354
37 atoms, 33 bonds, 5 residues, 1 model selected
> select add #37/A:353
45 atoms, 40 bonds, 6 residues, 1 model selected
> select add #37/A:352
56 atoms, 51 bonds, 7 residues, 1 model selected
> select add #37/A:351
64 atoms, 58 bonds, 8 residues, 1 model selected
> select add #37/A:350
69 atoms, 62 bonds, 9 residues, 1 model selected
> select add #37/A:349
73 atoms, 65 bonds, 10 residues, 1 model selected
> select add #37/A:348
78 atoms, 69 bonds, 11 residues, 1 model selected
> select add #37/A:347
83 atoms, 73 bonds, 12 residues, 1 model selected
> select add #37/A:346
92 atoms, 81 bonds, 13 residues, 1 model selected
> select add #37/A:345
99 atoms, 87 bonds, 14 residues, 1 model selected
> select add #37/A:344
103 atoms, 90 bonds, 15 residues, 1 model selected
> select add #37/A:341
111 atoms, 97 bonds, 16 residues, 1 model selected
> select add #37/A:342
120 atoms, 105 bonds, 17 residues, 1 model selected
> select add #37/A:343
129 atoms, 113 bonds, 18 residues, 1 model selected
> color sel red
> select clear
> hide #30 models
> show #30 models
> hide #30 models
> hide #!37 models
> show #!37 models
> select add #37
3984 atoms, 3982 bonds, 5 pseudobonds, 592 residues, 3 models selected
> select clear
[Repeated 2 time(s)]
> hide #37.1.1 models
> select #37/C: 195
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
[Repeated 1 time(s)]
> show #35 models
> hide #35 models
> select add #37/A:165
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #37/A:164
11 atoms, 9 bonds, 2 residues, 1 model selected
> select add #37/A:163
16 atoms, 13 bonds, 3 residues, 1 model selected
> select add #37/A:162
25 atoms, 21 bonds, 4 residues, 1 model selected
> select add #37/A:161
32 atoms, 27 bonds, 5 residues, 1 model selected
> select add #37/A:159
40 atoms, 34 bonds, 6 residues, 1 model selected
> select add #37/A:158
48 atoms, 41 bonds, 7 residues, 1 model selected
> select add #37/A:160
60 atoms, 53 bonds, 8 residues, 1 model selected
> select add #37/A:157
68 atoms, 60 bonds, 9 residues, 1 model selected
> select add #37/A:156
77 atoms, 68 bonds, 10 residues, 1 model selected
> select add #37/A:155
83 atoms, 73 bonds, 11 residues, 1 model selected
> select add #37/A:154
92 atoms, 81 bonds, 12 residues, 1 model selected
> select add #37/A:153
97 atoms, 85 bonds, 13 residues, 1 model selected
> select add #37/A:152
102 atoms, 89 bonds, 14 residues, 1 model selected
> select add #37/A:151
111 atoms, 97 bonds, 15 residues, 1 model selected
> select add #37/A:150
118 atoms, 103 bonds, 16 residues, 1 model selected
> select add #37/A:149
126 atoms, 110 bonds, 17 residues, 1 model selected
> color sel magenta
> select clear
> show #35 models
> show #30 models
> hide #!37 models
> select #30/B: 195
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> save "/Users/amy/Desktop/3C11_Fab_AAT_NE/make pictures/1oph_michaelis
> complex.jpg" width 935 height 668 supersample 3
> ui tool show Toolbar
> save /Users/amy/Desktop/image1.png supersample 3
> save "/Users/amy/Desktop/3C11_Fab_AAT_NE/make pictures/1oph_michaelis
> complex.png" width 935 height 668 supersample 3 transparentBackground true
> show #!37 models
> hide #30 models
> hide #35 models
> undo
> hide #35 models
> view
> hide #!37 models
> show #35 models
> show #!37 models
> hide #!37 models
> show #30 models
> save "/Users/amy/Desktop/3C11_Fab_AAT_NE/make pictures/1oph_michaelis
> complex.png" width 935 height 668 supersample 3 transparentBackground true
> hide #30 models
> hide #35 models
> show #!37 models
> save "/Users/amy/Desktop/3C11_Fab_AAT_NE/make pictures/1ezx_final
> complex.png" width 935 height 668 supersample 3 transparentBackground true
> save /Users/amy/Desktop/3C11_Fab_AAT_NE/csparc.cxs includeMaps true
——— End of log from Sun Feb 1 23:24:08 2026 ———
> view name session-start
opened ChimeraX session
> open 9hud fromDatabase pdb format mmcif
9hud title:
Alpha-1-antitrypsin in the cleaved conformation in complex with a
conformationally nonselective Fab fragment [more info...]
Chain information for 9hud #38
---
Chain | Description | UniProt
A C | Alpha-1-antitrypsin | A1AT_HUMAN 2-354
B D | Short peptide from AAT | A1AT_HUMAN 355-394
H I | FAB 9C5 heavy chain |
L M | FAB 9C5 light chain |
Non-standard residues in 9hud #38
---
CL — chloride ion
EDO — 1,2-ethanediol (ethylene glycol)
GLY — glycine
GOL — glycerol (glycerin; propane-1,2,3-triol)
LYS — lysine
NA — sodium ion
9hud mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
61 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
12039 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> hide #!37-38 cartoons
> show #!37-38 cartoons
> hide #!37-38 atoms
> select #38/A
2567 atoms, 2550 bonds, 398 residues, 1 model selected
> select #38/B
252 atoms, 251 bonds, 40 residues, 1 model selected
> select #38/C
2612 atoms, 2578 bonds, 415 residues, 1 model selected
> select #38/C,D
2873 atoms, 2840 bonds, 454 residues, 1 model selected
> delete #38/C,D
> select #38/H
1713 atoms, 1651 bonds, 322 residues, 1 model selected
> select #38/I
1736 atoms, 1654 bonds, 1 pseudobond, 338 residues, 2 models selected
> delete #38/I
> select #38/M
1766 atoms, 1691 bonds, 328 residues, 1 model selected
> delete #38/M
> hide #!37 models
> show #!37 models
> mmaker #38 to #37
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 1ezx, chain A (#37) with 9hud, chain A (#38), sequence alignment
score = 1674.4
RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
0.519)
> save /Users/amy/Desktop/3C11_Fab_AAT_NE/csparc.cxs includeMaps true
——— End of log from Wed Feb 11 13:24:40 2026 ———
> view name session-start
opened ChimeraX session
> open /Users/amy/Downloads/cryosparc_P483_J66_004_volume_map.mrc
Opened cryosparc_P483_J66_004_volume_map.mrc as #39, grid size 400,400,400,
pixel 0.723, shown at level 0.00725, step 2, values float32
> volume #39 level 0.0301
> hide #!37 models
> hide #!38 models
> volume #39 level 0.08437
> open /Users/amy/Downloads/cryosparc_P483_J69_005_volume_map.mrc
Opened cryosparc_P483_J69_005_volume_map.mrc as #40, grid size 400,400,400,
pixel 0.723, shown at level 0.00425, step 2, values float32
> volume #40 level 0.02603
> volume #40 level 0.05112
> transparency #40 50
> show #!39 models
> hide #!39 models
> show #!38 models
> select add #38
6282 atoms, 6138 bonds, 1077 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #38,-0.23813,0.96316,-0.12499,103.01,0.23278,-0.068345,-0.97012,107.01,-0.94292,-0.26011,-0.20793,320.16
> view matrix models
> #38,-0.35239,0.53131,-0.77041,145.72,-0.23758,-0.84704,-0.47549,205.11,-0.90519,0.015476,0.42472,295.71
> view matrix models
> #38,0.095516,0.64963,-0.75423,70.134,0.59254,-0.64594,-0.48131,66.164,-0.79986,-0.40094,-0.44663,305.92
> view matrix models
> #38,0.23814,0.79731,-0.5546,39.413,0.91725,-0.37235,-0.14145,0.058888,-0.31929,-0.47502,-0.82,237.42
> view matrix models
> #38,-0.29619,0.8953,-0.33273,117.39,0.7752,0.42884,0.46386,-15.784,0.55798,-0.12055,-0.82105,85.078
> view matrix models
> #38,-0.30596,0.51089,-0.80335,139.57,0.54659,0.78515,0.29115,8.8601,0.7795,-0.35003,-0.51948,55.076
> view matrix models
> #38,-0.30596,0.51089,-0.80335,160.4,0.54659,0.78515,0.29115,-4.0241,0.7795,-0.35003,-0.51948,56.001
> view matrix models
> #38,0.2554,0.95891,-0.12357,45.918,0.33368,0.032535,0.94213,50.395,0.90743,-0.28185,-0.31165,30.553
> view matrix models
> #38,0.28907,0.71313,0.63866,40.495,-0.045867,-0.65606,0.75332,139.21,0.95621,-0.24706,-0.15694,19.569
> view matrix models
> #38,0.66315,0.74847,0.0052223,-12.11,0.30094,-0.27301,0.91373,67.652,0.68532,-0.60437,-0.40629,79.243
> view matrix models
> #38,0.66315,0.74847,0.0052223,-14.717,0.30094,-0.27301,0.91373,95.231,0.68532,-0.60437,-0.40629,75.309
> view matrix models
> #38,0.66315,0.74847,0.0052223,9.7058,0.30094,-0.27301,0.91373,102.14,0.68532,-0.60437,-0.40629,70.114
> ui tool show "Fit in Map"
> fitmap #38 inMap #40
Fit molecule 9hud (#38) to map cryosparc_P483_J69_005_volume_map.mrc (#40)
using 6282 atoms
average map value = 0.0417, steps = 128
shifted from previous position = 4.51
rotated from previous position = 8.35 degrees
atoms outside contour = 4033, contour level = 0.051121
Position of 9hud (#38) relative to cryosparc_P483_J69_005_volume_map.mrc (#40)
coordinates:
Matrix rotation and translation
0.65684785 0.74878514 0.08872268 11.05139992
0.33454956 -0.39485965 0.85566491 105.25041377
0.67574218 -0.53235953 -0.50986845 72.64892317
Axis -0.88808312 -0.37558568 -0.26503541
Axis point 0.00000000 65.04529101 13.14028850
Rotation angle (degrees) 128.60443789
Shift along axis -68.59964747
> select subtract #38
Nothing selected
> volume #40 level 0.0597
> hide #!40 models
> show #!40 models
> hide #!38 models
> show #!38 models
> hide #!40 models
> show #!40 models
> hide #!38 models
> show #!38 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> show #!40 models
> hide #!38 models
> volume flip #40 axis z
Opened cryosparc_P483_J69_005_volume_map.mrc z flip as #41, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> show #!38 models
> select add #38
6282 atoms, 6138 bonds, 1077 residues, 1 model selected
> view matrix models
> #38,0.65685,0.74879,0.088723,12.679,0.33455,-0.39486,0.85566,109.56,0.67574,-0.53236,-0.50987,57.685
> view matrix models
> #38,-0.58254,0.54788,0.6004,210.02,0.59834,-0.2109,0.77299,61.815,0.55013,0.80954,-0.20496,22.25
> view matrix models
> #38,-0.40435,-0.85962,0.31233,239.45,0.49216,0.083334,0.86651,66.149,-0.7709,0.50409,0.38937,235.48
> view matrix models
> #38,-0.56895,-0.81456,0.11308,266.25,0.44686,-0.19079,0.87402,83.739,-0.69037,0.54781,0.47254,220.03
> view matrix models
> #38,-0.56895,-0.81456,0.11308,265.73,0.44686,-0.19079,0.87402,80.959,-0.69037,0.54781,0.47254,214.99
> fitmap #38 inMap #41
Fit molecule 9hud (#38) to map cryosparc_P483_J69_005_volume_map.mrc z flip
(#41) using 6282 atoms
average map value = 0.05473, steps = 216
shifted from previous position = 2.37
rotated from previous position = 33 degrees
atoms outside contour = 3800, contour level = 0.059703
Position of 9hud (#38) relative to cryosparc_P483_J69_005_volume_map.mrc z
flip (#41) coordinates:
Matrix rotation and translation
-0.75082147 -0.55505166 -0.35802903 289.09205452
0.04746292 -0.58599102 0.80892632 158.98706928
-0.65879769 0.59036614 0.46631901 208.65076835
Axis -0.30870385 0.42481867 0.85101765
Axis point 172.41915491 63.65569402 0.00000000
Rotation angle (degrees) 159.26804372
Shift along axis 155.86233044
> select subtract #38
Nothing selected
> volume #41 level 0.05159
> select add #38
6282 atoms, 6138 bonds, 1077 residues, 1 model selected
> view matrix models
> #38,-0.75082,-0.55505,-0.35803,289.14,0.047463,-0.58599,0.80893,158.79,-0.6588,0.59037,0.46632,207.97
> view matrix models
> #38,-0.75082,-0.55505,-0.35803,289.16,0.047463,-0.58599,0.80893,157.96,-0.6588,0.59037,0.46632,207.03
> view matrix models
> #38,-0.75082,-0.55505,-0.35803,288.72,0.047463,-0.58599,0.80893,155.88,-0.6588,0.59037,0.46632,205.57
> fitmap #38 inMap #41
Fit molecule 9hud (#38) to map cryosparc_P483_J69_005_volume_map.mrc z flip
(#41) using 6282 atoms
average map value = 0.05473, steps = 72
shifted from previous position = 4.4
rotated from previous position = 0.101 degrees
atoms outside contour = 3342, contour level = 0.051588
Position of 9hud (#38) relative to cryosparc_P483_J69_005_volume_map.mrc z
flip (#41) coordinates:
Matrix rotation and translation
-0.75090265 -0.55404999 -0.35940760 289.07011046
0.04645479 -0.58718152 0.80812117 159.19876899
-0.65877702 0.59012412 0.46665444 208.66676414
Axis -0.30899016 0.42432779 0.85115863
Axis point 172.44704823 63.68649423 0.00000000
Rotation angle (degrees) 159.34394496
Shift along axis 155.84115924
> view matrix models
> #38,-0.7509,-0.55405,-0.35941,287.93,0.046455,-0.58718,0.80812,155.5,-0.65878,0.59012,0.46665,206.09
> fitmap #38 inMap #41
Fit molecule 9hud (#38) to map cryosparc_P483_J69_005_volume_map.mrc z flip
(#41) using 6282 atoms
average map value = 0.05473, steps = 92
shifted from previous position = 4.65
rotated from previous position = 0.00364 degrees
atoms outside contour = 3341, contour level = 0.051588
Position of 9hud (#38) relative to cryosparc_P483_J69_005_volume_map.mrc z
flip (#41) coordinates:
Matrix rotation and translation
-0.75086696 -0.55406598 -0.35945751 289.07124867
0.04643032 -0.58719553 0.80811239 159.20847697
-0.65881943 0.59009517 0.46663119 208.66191835
Axis -0.30902059 0.42431965 0.85115164
Axis point 172.44904391 63.69342969 0.00000000
Rotation angle (degrees) 159.34407294
Shift along axis 155.82925281
> select subtract #38
Nothing selected
> combine #38 close false
> hide #!38 models
> select #42/A
2567 atoms, 2550 bonds, 398 residues, 1 model selected
> select #42/M
Nothing selected
> select #42/M
Nothing selected
> select #42/I
Nothing selected
> select #42/H
1713 atoms, 1651 bonds, 322 residues, 1 model selected
> delete #42/H
> select #42/N
Nothing selected
> select #42/I
Nothing selected
> select #42/L
1750 atoms, 1686 bonds, 317 residues, 1 model selected
> delete #42/L
> fitmap #42 inMap #41
Fit molecule copy of 9hud (#42) to map cryosparc_P483_J69_005_volume_map.mrc z
flip (#41) using 2819 atoms
average map value = 0.06533, steps = 56
shifted from previous position = 0.821
rotated from previous position = 3.38 degrees
atoms outside contour = 1262, contour level = 0.051588
Position of copy of 9hud (#42) relative to
cryosparc_P483_J69_005_volume_map.mrc z flip (#41) coordinates:
Matrix rotation and translation
-0.73693347 -0.57914780 -0.34859273 288.27078922
0.03048667 -0.54364745 0.83875981 157.64342584
-0.67527744 0.60748274 0.41828829 210.31462354
Axis -0.31712566 0.44794803 0.83592696
Axis point 174.06638485 60.58096428 0.00000000
Rotation angle (degrees) 158.61421520
Shift along axis 155.00566094
> volume #41 level 0.06516
> select add #42
2819 atoms, 2801 bonds, 438 residues, 1 model selected
> view matrix models
> #42,-0.73693,-0.57915,-0.34859,287.85,0.030487,-0.54365,0.83876,156.54,-0.67528,0.60748,0.41829,208.51
> fitmap #42 inMap #41
Fit molecule copy of 9hud (#42) to map cryosparc_P483_J69_005_volume_map.mrc z
flip (#41) using 2819 atoms
average map value = 0.06533, steps = 76
shifted from previous position = 2.15
rotated from previous position = 0.0105 degrees
atoms outside contour = 1566, contour level = 0.065161
Position of copy of 9hud (#42) relative to
cryosparc_P483_J69_005_volume_map.mrc z flip (#41) coordinates:
Matrix rotation and translation
-0.73689140 -0.57919551 -0.34860239 288.27541199
0.03038436 -0.54353165 0.83883856 157.64897324
-0.67532796 0.60754087 0.41812229 210.31189981
Axis -0.31716299 0.44801683 0.83587592
Axis point 174.07498439 60.57428048 0.00000000
Rotation angle (degrees) 158.61485484
Shift along axis 154.99375355
> view matrix models
> #42,-0.73689,-0.5792,-0.3486,286.89,0.030384,-0.54353,0.83884,156.41,-0.67533,0.60754,0.41812,208.9
> view matrix models
> #42,-0.73689,-0.5792,-0.3486,287.57,0.030384,-0.54353,0.83884,158.73,-0.67533,0.60754,0.41812,212.26
> view matrix models
> #42,-0.73689,-0.5792,-0.3486,287.63,0.030384,-0.54353,0.83884,158.66,-0.67533,0.60754,0.41812,212.24
> fitmap #42 inMap #41
Fit molecule copy of 9hud (#42) to map cryosparc_P483_J69_005_volume_map.mrc z
flip (#41) using 2819 atoms
average map value = 0.06533, steps = 76
shifted from previous position = 2.27
rotated from previous position = 0.0141 degrees
atoms outside contour = 1565, contour level = 0.065161
Position of copy of 9hud (#42) relative to
cryosparc_P483_J69_005_volume_map.mrc z flip (#41) coordinates:
Matrix rotation and translation
-0.73682803 -0.57935101 -0.34847792 288.27467210
0.03043622 -0.54334125 0.83896003 157.62886136
-0.67539477 0.60756292 0.41798231 210.32004980
Axis -0.31717295 0.44810058 0.83582725
Axis point 174.07853761 60.56677345 0.00000000
Rotation angle (degrees) 158.60591524
Shift along axis 154.99188631
> select subtract #42
Nothing selected
> show #!38 models
> mmaker #38 to #42
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 copy of 9hud, chain A (#42) with 9hud, chain A (#38), sequence
alignment score = 1849.2
RMSD between 332 pruned atom pairs is 0.000 angstroms; (across all 332 pairs:
0.000)
> hide #!42 models
> hide #!38 models
> show #!38 models
> show #!37 models
> mmaker #37 to #38
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 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
score = 1674.4
RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
0.519)
> open /Users/amy/Downloads/cryosparc_P483_J81_008_volume_map.mrc
Opened cryosparc_P483_J81_008_volume_map.mrc as #43, grid size 400,400,400,
pixel 0.723, shown at level 0.00732, step 2, values float32
> hide #!37 models
> hide #!38 models
> hide #!41 models
> surface dust #43 size 7.23
> volume #43 level 0.06119
> volume #43 level 0.0273
> volume flip #43 axis z
Opened cryosparc_P483_J81_008_volume_map.mrc z flip as #44, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> transparency #44 50
> volume #44 level 0.03941
> volume #44 level 0.04042
> open /Users/amy/Downloads/cryosparc_P483_J66_004_volume_map.mrc
Opened cryosparc_P483_J66_004_volume_map.mrc as #45, grid size 400,400,400,
pixel 0.723, shown at level 0.00725, step 2, values float32
> volume #45 level 0.06094
> open /Users/amy/Downloads/cryosparc_P483_J72_006_volume_map.mrc
Opened cryosparc_P483_J72_006_volume_map.mrc as #46, grid size 400,400,400,
pixel 0.723, shown at level 0.0048, step 2, values float32
> volume #46 level 0.04807
> transparency #46 50
> show #!42 models
> hide #!42 models
> show #!38 models
> select add #38
6282 atoms, 6138 bonds, 1077 residues, 1 model selected
> view matrix models
> #38,-0.73683,-0.57935,-0.34848,292.33,0.030436,-0.54334,0.83896,164.74,-0.67539,0.60756,0.41798,237.37
> view matrix models
> #38,-0.38309,-0.69929,0.60352,229.08,0.62032,0.28936,0.72902,40.857,-0.68443,0.65365,0.32294,238.22
> view matrix models
> #38,-0.38309,-0.69929,0.60352,226.04,0.62032,0.28936,0.72902,38.256,-0.68443,0.65365,0.32294,241.06
> view matrix models
> #38,-0.34943,-0.72907,0.58852,222.05,0.61787,0.29288,0.72969,38.499,-0.70437,0.61861,0.34813,245.24
> view matrix models
> #38,-0.34943,-0.72907,0.58852,222.59,0.61787,0.29288,0.72969,38.714,-0.70437,0.61861,0.34813,242.8
> fitmap #38 inMap #46
Fit molecule 9hud (#38) to map cryosparc_P483_J72_006_volume_map.mrc (#46)
using 6282 atoms
average map value = 0.0399, steps = 112
shifted from previous position = 6.23
rotated from previous position = 3.87 degrees
atoms outside contour = 3940, contour level = 0.048075
Position of 9hud (#38) relative to cryosparc_P483_J72_006_volume_map.mrc (#46)
coordinates:
Matrix rotation and translation
-0.34701016 -0.76389374 0.54410505 226.91723804
0.57651318 0.28385608 0.76619729 40.13005322
-0.73974084 0.57956197 0.34189387 251.72894877
Axis -0.10005014 0.68823502 0.71855586
Axis point 172.83638513 16.61736328 0.00000000
Rotation angle (degrees) 111.13889774
Shift along axis 185.79711858
> select subtract #38
Nothing selected
> volume flip #46 axis z
Opened cryosparc_P483_J72_006_volume_map.mrc z flip as #47, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> select add #38
6282 atoms, 6138 bonds, 1077 residues, 1 model selected
> view matrix models
> #38,-0.43781,-0.43705,0.78569,225.72,0.89875,-0.18935,0.39548,11.956,-0.024068,0.87928,0.47569,125.36
> view matrix models
> #38,0.17782,0.26753,0.947,99.291,0.050808,-0.96355,0.26266,177.44,0.98275,0.001409,-0.18493,8.0567
> view matrix models
> #38,0.17782,0.26753,0.947,103.63,0.050808,-0.96355,0.26266,172.68,0.98275,0.001409,-0.18493,-1.716
> view matrix models
> #38,0.63642,0.20154,0.74455,36.153,-0.42467,-0.71425,0.55633,234.65,0.64391,-0.67025,-0.36898,79.951
> view matrix models
> #38,0.63642,0.20154,0.74455,34.766,-0.42467,-0.71425,0.55633,241.95,0.64391,-0.67025,-0.36898,57.4
> fitmap #38 inMap #47
Fit molecule 9hud (#38) to map cryosparc_P483_J72_006_volume_map.mrc z flip
(#47) using 6282 atoms
average map value = 0.06343, steps = 124
shifted from previous position = 5.23
rotated from previous position = 14 degrees
atoms outside contour = 2477, contour level = 0.048075
Position of 9hud (#38) relative to cryosparc_P483_J72_006_volume_map.mrc z
flip (#47) coordinates:
Matrix rotation and translation
0.48056680 0.06585233 0.87448215 60.37965921
-0.56537086 -0.73901641 0.36634758 262.76707770
0.67038150 -0.67046120 -0.31791576 52.06857630
Axis -0.84232947 0.16581649 -0.51282156
Axis point 0.00000000 144.40291810 -47.17976586
Rotation angle (degrees) 142.01600325
Shift along axis -33.99034036
> select subtract #38
Nothing selected
> hide #!47 models
> show #!47 models
> hide #!38 models
> show #!38 models
> hide #!38 models
> hide #!45 models
> show #!44 models
> show #!38 models
> select add #38
6282 atoms, 6138 bonds, 1077 residues, 1 model selected
> view matrix models
> #38,0.48057,0.065852,0.87448,65.866,-0.56537,-0.73902,0.36635,260.8,0.67038,-0.67046,-0.31792,67.074
> view matrix models
> #38,0.24561,0.13628,0.95974,99.26,-0.61016,-0.7476,0.2623,269.51,0.75324,-0.65002,-0.10047,50.465
> view matrix models
> #38,0.24561,0.13628,0.95974,97.908,-0.61016,-0.7476,0.2623,267.42,0.75324,-0.65002,-0.10047,51.929
> fitmap #38 inMap #44
Fit molecule 9hud (#38) to map cryosparc_P483_J81_008_volume_map.mrc z flip
(#44) using 6282 atoms
average map value = 0.03783, steps = 168
shifted from previous position = 5.42
rotated from previous position = 16.7 degrees
atoms outside contour = 3802, contour level = 0.040419
Position of 9hud (#38) relative to cryosparc_P483_J81_008_volume_map.mrc z
flip (#44) coordinates:
Matrix rotation and translation
0.06820670 -0.05795023 0.99598676 133.26750912
-0.73706857 -0.67572583 0.01115934 290.51260544
0.67236729 -0.73487167 -0.08880232 64.60372631
Axis -0.70414963 0.30545181 -0.64099336
Axis point 0.00000000 181.24183814 -90.37493056
Rotation angle (degrees) 148.01217964
Shift along axis -46.51322447
> select subtract #38
Nothing selected
> hide #!44 models
> show #!43 models
> transparency #38 50
> transparency #43 50
> select add #38
6282 atoms, 6138 bonds, 1077 residues, 1 model selected
> view matrix models
> #38,-0.34778,-0.62711,0.69698,224.64,0.7034,0.317,0.6362,16.77,-0.61991,0.71151,0.33086,208.25
> view matrix models
> #38,-0.34778,-0.62711,0.69698,225.83,0.7034,0.317,0.6362,17.542,-0.61991,0.71151,0.33086,207.48
> view matrix models
> #38,-0.28771,-0.41373,0.86374,206.06,0.80892,0.37784,0.45043,0.83954,-0.51271,0.82829,0.22596,187.36
> view matrix models
> #38,-0.28771,-0.41373,0.86374,206.43,0.80892,0.37784,0.45043,-2.4203,-0.51271,0.82829,0.22596,194.27
> view matrix models
> #38,-0.43329,-0.6387,0.63587,240.94,0.33837,0.53864,0.77161,61.821,-0.83533,0.54948,-0.01727,259.04
> view matrix models
> #38,-0.43329,-0.6387,0.63587,240.15,0.33837,0.53864,0.77161,62.236,-0.83533,0.54948,-0.01727,256.27
> view matrix models
> #38,-0.10971,-0.34204,0.93326,173.87,0.39597,0.84616,0.35667,46.512,-0.91169,0.40867,0.042608,273
> view matrix models
> #38,-0.10971,-0.34204,0.93326,174.05,0.39597,0.84616,0.35667,43.272,-0.91169,0.40867,0.042608,270.13
> hide #!43 models
> show #!44 models
> view matrix models
> #38,0.33372,0.10106,0.93724,86.86,-0.90444,-0.24596,0.34856,290.96,0.26575,-0.964,0.009315,136.98
> view matrix models
> #38,-0.0077799,0.047421,0.99884,142.16,-0.55565,-0.83068,0.035109,262.15,0.83138,-0.55473,0.032812,31.52
> view matrix models
> #38,-0.0077799,0.047421,0.99884,141.96,-0.55565,-0.83068,0.035109,262.22,0.83138,-0.55473,0.032812,29.958
> fitmap #38 inMap #44
Fit molecule 9hud (#38) to map cryosparc_P483_J81_008_volume_map.mrc z flip
(#44) using 6282 atoms
average map value = 0.03751, steps = 112
shifted from previous position = 5.86
rotated from previous position = 9.02 degrees
atoms outside contour = 3835, contour level = 0.040419
Position of 9hud (#38) relative to cryosparc_P483_J81_008_volume_map.mrc z
flip (#44) coordinates:
Matrix rotation and translation
0.05690807 -0.02329864 0.99810753 137.02419950
-0.65514588 -0.75524488 0.01972424 280.23565345
0.75335606 -0.65502851 -0.05824354 46.13973405
Axis -0.70561938 0.25594766 -0.66075116
Axis point 0.00000000 166.68305562 -94.19367789
Rotation angle (degrees) 151.43679087
Shift along axis -55.44815397
> select subtract #38
Nothing selected
> select add #38
6282 atoms, 6138 bonds, 1077 residues, 1 model selected
> view matrix models
> #38,-0.54924,-0.83446,0.044834,275.94,-0.071518,-0.0065171,-0.99742,171.91,0.8326,-0.55103,-0.0561,29.588
> view matrix models
> #38,-0.095818,-0.5899,-0.80177,205.42,-0.19261,0.80124,-0.56649,154.68,0.97659,0.10015,-0.1904,-16.494
> view matrix models
> #38,-0.39728,-0.77299,0.49462,243.92,-0.63802,-0.15476,-0.75431,264.16,0.65962,-0.61525,-0.4317,64.108
> view matrix models
> #38,0.28514,0.071787,0.95579,97.806,-0.70813,-0.65625,0.26054,281.81,0.64594,-0.75112,-0.13629,67.792
> view matrix models
> #38,0.28514,0.071787,0.95579,96.286,-0.70813,-0.65625,0.26054,282.4,0.64594,-0.75112,-0.13629,66.958
> fitmap #38 inMap #44
Fit molecule 9hud (#38) to map cryosparc_P483_J81_008_volume_map.mrc z flip
(#44) using 6282 atoms
average map value = 0.03783, steps = 168
shifted from previous position = 3.71
rotated from previous position = 14.8 degrees
atoms outside contour = 3801, contour level = 0.040419
Position of 9hud (#38) relative to cryosparc_P483_J81_008_volume_map.mrc z
flip (#44) coordinates:
Matrix rotation and translation
0.06820710 -0.05791598 0.99598872 133.26635838
-0.73705893 -0.67573598 0.01118160 290.51125280
0.67237782 -0.73486504 -0.08877748 64.60105058
Axis -0.70414832 0.30543677 -0.64100197
Axis point 0.00000000 181.23877487 -90.37820158
Rotation angle (degrees) 148.01136342
Shift along axis -46.51586553
> select subtract #38
Nothing selected
> show #35 models
> select add #35
5953 atoms, 5684 bonds, 699 residues, 1 model selected
> view matrix models
> #35,-0.44103,0.30301,0.84479,116.92,-0.07491,-0.95043,0.30179,113.9,0.89436,0.069815,0.44187,126.48
> view matrix models
> #35,0.84908,-0.51887,-0.099238,120.01,0.43126,0.7893,-0.43705,123.08,0.3051,0.3283,0.89394,124.61
> mmaker #35 to #38
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 9hud, chain A (#38) with 8pi2, chain A (#35), sequence alignment
score = 1753.4
RMSD between 220 pruned atom pairs is 0.913 angstroms; (across all 331 pairs:
6.169)
> hide #!38 models
> fitmap #35 inMap #44
Fit molecule 8pi2 (#35) to map cryosparc_P483_J81_008_volume_map.mrc z flip
(#44) using 5953 atoms
average map value = 0.03426, steps = 124
shifted from previous position = 5.39
rotated from previous position = 16.8 degrees
atoms outside contour = 3776, contour level = 0.040419
Position of 8pi2 (#35) relative to cryosparc_P483_J81_008_volume_map.mrc z
flip (#44) coordinates:
Matrix rotation and translation
-0.91986475 0.28876257 0.26545250 167.24012801
0.39170890 0.64122785 0.65984164 130.22015692
0.02032204 0.71094517 -0.70295376 131.41006954
Axis 0.18875717 0.90541952 0.38024495
Axis point 72.13306632 0.00000000 33.49476567
Rotation angle (degrees) 172.22007439
Shift along axis 199.43966055
> mmaker #35 to #38
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 9hud, chain A (#38) with 8pi2, chain A (#35), sequence alignment
score = 1753.4
RMSD between 220 pruned atom pairs is 0.913 angstroms; (across all 331 pairs:
6.169)
> select subtract #35
Nothing selected
> hide #!44 models
> show #!44 models
> hide #35 models
> show #!38 models
> show #!37 models
> mmaker #37 to #38
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 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
score = 1674.4
RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
0.519)
> hide #!38 models
> show #!38 models
> hide #!37 models
> hide #!38 models
> hide #!44 models
> show #!47 models
> show #!38 models
> select add #38
6282 atoms, 6138 bonds, 1077 residues, 1 model selected
> view matrix models
> #38,0.12454,-0.84591,0.51858,160.56,-0.95063,-0.25145,-0.18186,310.42,0.28423,-0.47033,-0.83547,125.18
> view matrix models
> #38,0.67023,0.035917,0.74129,37.629,-0.48282,-0.73746,0.47227,246.9,0.56363,-0.67443,-0.47692,84.334
> view matrix models
> #38,0.67023,0.035917,0.74129,35.095,-0.48282,-0.73746,0.47227,252.87,0.56363,-0.67443,-0.47692,70.069
> view matrix models
> #38,0.72811,0.043332,0.68409,26.371,-0.55319,-0.55218,0.62376,255,0.40477,-0.8326,-0.37807,100.03
> view matrix models
> #38,0.72811,0.043332,0.68409,24.921,-0.55319,-0.55218,0.62376,251.59,0.40477,-0.8326,-0.37807,100.94
> fitmap #38 inMap #47
Fit molecule 9hud (#38) to map cryosparc_P483_J72_006_volume_map.mrc z flip
(#47) using 6282 atoms
average map value = 0.06343, steps = 212
shifted from previous position = 1.3
rotated from previous position = 22.3 degrees
atoms outside contour = 2481, contour level = 0.048075
Position of 9hud (#38) relative to cryosparc_P483_J72_006_volume_map.mrc z
flip (#47) coordinates:
Matrix rotation and translation
0.48048529 0.06576118 0.87453379 60.39061577
-0.56539285 -0.73906673 0.36621209 262.77340318
0.67042137 -0.67041468 -0.31792978 52.06026777
Axis -0.84230945 0.16585123 -0.51284322
Axis point 0.00000000 144.40605826 -47.18056764
Rotation angle (degrees) 142.02279334
Shift along axis -33.98504950
> select subtract #38
Nothing selected
> volume #47 level 0.05522
> volume #47 level 0.04807
> show #!37 models
> mmaker #37 to #38
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 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
score = 1674.4
RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
0.519)
> volume #47 level 0.0495
> volume #47 level 0.01949
> volume #47 level 0.02878
> volume gaussian #47 sDev 2
Opened cryosparc_P483_J72_006_volume_map.mrc z flip gaussian as #48, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> volume #48 level 0.002656
> volume #48 level 0.001381
> surface dust #48 size 7.23
> show #!44 models
> hide #!38 models
> hide #!37 models
> volume gaussian #44 sDev 2
Opened cryosparc_P483_J81_008_volume_map.mrc z flip gaussian as #49, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> surface dust #49 size 7.23
> volume #49 level 0.01018
Cell requested for row 3 is out of bounds for table with 3 rows! Resizing
table model.
> save "/Users/amy/Desktop/SPA AAT_HNE/9C5_Fab_AAT_HNE/For mask
> generation/hne_J81localrefine.mrc" models #49
> volume #49 level 0.01049
> open /Users/amy/Downloads/cryosparc_P483_J82_005_volume_map.mrc
Opened cryosparc_P483_J82_005_volume_map.mrc as #50, grid size 400,400,400,
pixel 0.723, shown at level 0.00546, step 2, values float32
> volume #50 level 0.0526
> open /Users/amy/Downloads/cryosparc_P483_J90_004_volume_map.mrc
Opened cryosparc_P483_J90_004_volume_map.mrc as #51, grid size 400,400,400,
pixel 0.723, shown at level 0.00654, step 2, values float32
> surface dust #51 size 7.23
> volume #51 level 0.03836
> open /Users/amy/Downloads/cryosparc_P483_J89_003_volume_map.mrc
Opened cryosparc_P483_J89_003_volume_map.mrc as #52, grid size 400,400,400,
pixel 0.723, shown at level 0.00398, step 2, values float32
> volume #52 level 0.01728
> volume #52 level 0.004928
> hide #!52 models
> show #!44 models
> open /Users/amy/Downloads/cryosparc_P483_J93_005_volume_map.mrc
Opened cryosparc_P483_J93_005_volume_map.mrc as #53, grid size 400,400,400,
pixel 0.723, shown at level 0.00624, step 2, values float32
> volume #53 level 0.03597
> open /Users/amy/Downloads/cryosparc_P483_J96_002_volume_map.mrc
Opened cryosparc_P483_J96_002_volume_map.mrc as #54, grid size 400,400,400,
pixel 0.723, shown at level 0.00203, step 2, values float32
> volume #54 level 0.01882
> volume #54 level 0.01406
> open /Users/amy/Downloads/cryosparc_P483_J99_003_volume_map.mrc
Opened cryosparc_P483_J99_003_volume_map.mrc as #55, grid size 400,400,400,
pixel 0.723, shown at level 0.00233, step 2, values float32
> surface dust #55 size 7.23
> volume #55 level 0.011
> ui mousemode right "tape measure"
> marker segment #56 position 137.9,161.4,84.92 toPosition 127.8,150.1,133.2
> color yellow radius 0.1807 label 50.59 labelHeight 5.059 labelColor yellow
> marker segment #56 position 137.6,155.7,84.27 toPosition 148.8,133.1,193.5
> color yellow radius 0.1807 label 112.1 labelHeight 11.21 labelColor yellow
> marker segment #56 position 139,177,192 toPosition 130,91.37,164 color
> yellow radius 0.1807 label 90.59 labelHeight 9.059 labelColor yellow
> close #56
> transparency #55 50
> show #!38 models
> select add #38
6282 atoms, 6138 bonds, 1077 residues, 1 model selected
> select subtract #38
Nothing selected
> volume flip #55 axis z
Opened cryosparc_P483_J99_003_volume_map.mrc z flip as #56, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> transparency #56 50
> select add #38
6282 atoms, 6138 bonds, 1077 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #38,0.48049,0.065761,0.87453,61.743,-0.56539,-0.73907,0.36621,262.06,0.67042,-0.67041,-0.31793,59.233
> view matrix models
> #38,0.61181,-0.23623,0.75491,54.055,-0.64298,-0.70439,0.30068,273.82,0.46072,-0.66935,-0.58285,95.671
> view matrix models
> #38,0.50154,0.032674,0.86452,59.807,-0.035285,-0.99768,0.058177,191.99,0.86441,-0.059683,-0.49923,7.3804
> view matrix models
> #38,0.50154,0.032674,0.86452,52.131,-0.035285,-0.99768,0.058177,176.02,0.86441,-0.059683,-0.49923,12.857
> view matrix models
> #38,0.35345,0.1643,0.92091,69.799,-0.028974,-0.98206,0.18633,172.82,0.93501,-0.09254,-0.34235,0.99177
> view matrix models
> #38,0.66671,0.39133,0.63431,15.122,-0.22913,-0.70224,0.67407,187.64,0.70922,-0.59475,-0.37853,56.427
> view matrix models
> #38,0.66671,0.39133,0.63431,20.436,-0.22913,-0.70224,0.67407,208.21,0.70922,-0.59475,-0.37853,56.608
> view matrix models
> #38,0.81008,0.3223,0.48979,2.2149,-0.16331,-0.67827,0.71643,196.35,0.56311,-0.66036,-0.49682,83.714
> fitmap #38 inMap #56
Fit molecule 9hud (#38) to map cryosparc_P483_J99_003_volume_map.mrc z flip
(#56) using 6282 atoms
average map value = 0.03831, steps = 132
shifted from previous position = 1.92
rotated from previous position = 15.8 degrees
atoms outside contour = 568, contour level = 0.011004
Position of 9hud (#38) relative to cryosparc_P483_J99_003_volume_map.mrc z
flip (#56) coordinates:
Matrix rotation and translation
0.71987433 0.56582857 0.40201864 5.33395219
-0.00113467 -0.57823035 0.81587277 166.00801694
0.69410350 -0.58778202 -0.41561115 58.96322716
Axis -0.91042678 -0.18944963 -0.36773893
Axis point 0.00000000 92.18313505 -11.68775993
Rotation angle (degrees) 129.56725904
Shift along axis -57.98940372
> select subtract #38
Nothing selected
> show #!37 models
> mmaker #38 to #37
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 1ezx, chain A (#37) with 9hud, chain A (#38), sequence alignment
score = 1674.4
RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
0.519)
> select add #38
6282 atoms, 6138 bonds, 1077 residues, 1 model selected
> view matrix models
> #38,0.48049,0.065761,0.87453,62.141,-0.56539,-0.73907,0.36621,264.84,0.67042,-0.67041,-0.31793,61.109
> view matrix models
> #38,0.48049,0.065761,0.87453,61.431,-0.56539,-0.73907,0.36621,264.59,0.67042,-0.67041,-0.31793,64.599
> fitmap #38 inMap #56
Fit molecule 9hud (#38) to map cryosparc_P483_J99_003_volume_map.mrc z flip
(#56) using 6282 atoms
average map value = 0.03831, steps = 216
shifted from previous position = 1.65
rotated from previous position = 43.4 degrees
atoms outside contour = 569, contour level = 0.011004
Position of 9hud (#38) relative to cryosparc_P483_J99_003_volume_map.mrc z
flip (#56) coordinates:
Matrix rotation and translation
0.71990687 0.56573446 0.40209280 5.32940054
-0.00119592 -0.57831351 0.81581374 166.01905071
0.69406964 -0.58779078 -0.41565530 58.96739860
Axis -0.91044042 -0.18938918 -0.36773629
Axis point 0.00000000 92.19051844 -11.68521420
Rotation angle (degrees) 129.57078110
Shift along axis -57.97876700
> select subtract #38
Nothing selected
> show #!39 models
> hide #!39 models
> show #!37 models
> mmaker #37 to #38
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 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
score = 1674.4
RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
0.519)
> volume #56 level 0.007481
> show #!42 models
> hide #!42 models
> combine #37 close false
> hide #!57.1 models
> hide #!37 models
> show #!37 models
> hide #!38 models
> hide #!37 models
> select #57/A
2686 atoms, 2674 bonds, 398 residues, 1 model selected
> delete #57/A
> select #57/B
289 atoms, 294 bonds, 39 residues, 1 model selected
> delete #57/B
> show #!37 models
> show #!38 models
> fitmap #57 inMap #56
Fit molecule copy of 1ezx (#57) to map cryosparc_P483_J99_003_volume_map.mrc z
flip (#56) using 1009 atoms
average map value = 0.01739, steps = 256
shifted from previous position = 13.8
rotated from previous position = 53.3 degrees
atoms outside contour = 290, contour level = 0.0074814
Position of copy of 1ezx (#57) relative to
cryosparc_P483_J99_003_volume_map.mrc z flip (#56) coordinates:
Matrix rotation and translation
0.75779051 -0.13010105 0.63939601 57.96350024
0.04649693 0.98819623 0.14596657 79.83854912
-0.65083914 -0.08088213 0.75489502 138.89870189
Axis -0.17161128 0.97606430 0.13359657
Axis point 208.75729766 0.00000000 -34.80031847
Rotation angle (degrees) 41.37141702
Shift along axis 86.53675668
> hide #!38 models
> hide #!37 models
> show #!37 models
> hide #!37 models
> show #!38 models
> show #!47 models
> hide #!56 models
> hide #!57 models
> hide #!47 models
> open /Users/amy/Downloads/cryosparc_P483_J103_003_volume_map.mrc
Opened cryosparc_P483_J103_003_volume_map.mrc as #58, grid size 400,400,400,
pixel 0.723, shown at level 0.00468, step 2, values float32
> surface dust #58 size 7.23
> volume #58 level 0.01873
> transparency #58 50
> select add #38
6282 atoms, 6138 bonds, 1077 residues, 1 model selected
> view matrix models
> #38,0.79207,-0.60151,-0.10399,45.033,0.096519,-0.044809,0.99432,127.86,-0.60276,-0.79761,0.022565,266.66
> view matrix models
> #38,-0.14652,-0.85779,0.49268,195.86,0.54759,0.34445,0.76256,44.475,-0.82382,0.38152,0.41925,251.42
> view matrix models
> #38,-0.14652,-0.85779,0.49268,198.48,0.54759,0.34445,0.76256,48.533,-0.82382,0.38152,0.41925,263.76
> view matrix models
> #38,-0.14652,-0.85779,0.49268,194.13,0.54759,0.34445,0.76256,44.618,-0.82382,0.38152,0.41925,261.43
> view matrix models
> #38,-0.10749,-0.76087,0.63994,182.4,0.68336,0.41097,0.60342,22.58,-0.72212,0.50217,0.47577,240.01
> volume flip #58 axis z
Opened cryosparc_P483_J103_003_volume_map.mrc z flip as #59, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> view matrix models
> #38,0.47388,0.52578,0.70639,40.242,-0.49413,-0.50521,0.70753,242.68,0.72888,-0.68433,0.020401,61.728
> view matrix models
> #38,0.47388,0.52578,0.70639,38.39,-0.49413,-0.50521,0.70753,241.35,0.72888,-0.68433,0.020401,61.925
> view matrix models
> #38,0.62595,0.63777,0.44881,13.26,-0.13423,-0.47881,0.8676,181.41,0.76822,-0.60332,-0.2141,55.525
> view matrix models
> #38,0.62595,0.63777,0.44881,16.43,-0.13423,-0.47881,0.8676,181.76,0.76822,-0.60332,-0.2141,47.364
> view matrix models
> #38,0.62595,0.63777,0.44881,20.934,-0.13423,-0.47881,0.8676,183.19,0.76822,-0.60332,-0.2141,39.547
> fitmap #38 inMap #59
Fit molecule 9hud (#38) to map cryosparc_P483_J103_003_volume_map.mrc z flip
(#59) using 6282 atoms
average map value = 0.04126, steps = 168
shifted from previous position = 5.69
rotated from previous position = 19.5 degrees
atoms outside contour = 1297, contour level = 0.018732
Position of 9hud (#38) relative to cryosparc_P483_J103_003_volume_map.mrc z
flip (#59) coordinates:
Matrix rotation and translation
0.70777878 0.35342642 0.61166899 13.30926304
-0.29975381 -0.63379066 0.71306173 215.20863100
0.63968496 -0.68804008 -0.34264266 66.23170214
Axis -0.90619968 -0.01812007 -0.42246160
Axis point 0.00000000 119.91219967 -25.94584346
Rotation angle (degrees) 129.37010768
Shift along axis -43.94079555
> mmaker #37 to #38
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 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
score = 1674.4
RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
0.519)
> select subtract #38
Nothing selected
> show #!37 models
> show #!57 models
> mmaker #57 to #37
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 1ezx, chain C (#37) with copy of 1ezx, chain C (#57), sequence
alignment score = 1096
RMSD between 140 pruned atom pairs is 0.000 angstroms; (across all 140 pairs:
0.000)
> hide #!37 models
> select #57/A
Nothing selected
> select #57/C
1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 2 models selected
> select #57/C: 202
6 atoms, 5 bonds, 1 residue, 1 model selected
> show #!37 models
> ui tool show "Show Sequence Viewer"
> select #57/C: 197
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #57/C: 195
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #57
1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 3 models selected
> select subtract #57
Nothing selected
> hide #!37 models
> select add #57
1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 3 models selected
> fitmap #57 inMap #59
Fit molecule copy of 1ezx (#57) to map cryosparc_P483_J103_003_volume_map.mrc
z flip (#59) using 1009 atoms
average map value = 0.03856, steps = 332
shifted from previous position = 30.6
rotated from previous position = 62.2 degrees
atoms outside contour = 286, contour level = 0.018732
Position of copy of 1ezx (#57) relative to
cryosparc_P483_J103_003_volume_map.mrc z flip (#59) coordinates:
Matrix rotation and translation
0.57046373 0.04988227 0.81980662 55.55575937
-0.78184304 0.33872670 0.52343642 167.07972587
-0.25158019 -0.93956159 0.23223140 158.05911115
Axis -0.73333465 0.53703769 -0.41690623
Axis point 0.00000000 214.40037540 -65.68721584
Rotation angle (degrees) 85.94517935
Shift along axis -16.90868204
> view matrix models
> #57,0.57046,0.049882,0.81981,53.391,-0.78184,0.33873,0.52344,146.96,-0.25158,-0.93956,0.23223,152.39
> view matrix models
> #57,0.57046,0.049882,0.81981,51.548,-0.78184,0.33873,0.52344,139.36,-0.25158,-0.93956,0.23223,150.37
> view matrix models
> #57,0.60961,0.26554,0.74691,47.106,-0.77216,0.41204,0.48373,138.91,-0.17931,-0.87162,0.45622,131.48
> view matrix models
> #57,0.60961,0.26554,0.74691,46.208,-0.77216,0.41204,0.48373,140.83,-0.17931,-0.87162,0.45622,128.81
> view matrix models
> #57,0.49766,0.67771,0.54133,56.234,-0.85191,0.49924,0.15817,161.92,-0.16306,-0.53988,0.8258,100.9
> view matrix models
> #57,0.49766,0.67771,0.54133,55.941,-0.85191,0.49924,0.15817,159.37,-0.16306,-0.53988,0.8258,99.317
> view matrix models
> #57,0.83968,0.36634,0.40093,42.637,-0.49094,0.82767,0.27193,116.69,-0.23222,-0.42516,0.87482,99.752
> hide #!57 models
> select subtract #57
Nothing selected
> hide #!59 models
> show #!47 models
> fitmap #38 inMap #47
Fit molecule 9hud (#38) to map cryosparc_P483_J72_006_volume_map.mrc z flip
(#47) using 6282 atoms
average map value = 0.06343, steps = 180
shifted from previous position = 8.63
rotated from previous position = 26.1 degrees
atoms outside contour = 1606, contour level = 0.028781
Position of 9hud (#38) relative to cryosparc_P483_J72_006_volume_map.mrc z
flip (#47) coordinates:
Matrix rotation and translation
0.48062832 0.06570846 0.87445915 60.38102135
-0.56537857 -0.73904318 0.36628165 262.76806751
0.67033088 -0.67044580 -0.31805493 52.08064169
Axis -0.84235493 0.16585696 -0.51276666
Axis point 0.00000000 144.40697546 -47.16273001
Rotation angle (degrees) 142.02086420
Shift along axis -33.98555515
> show #35 models
> mmaker #35 to #38
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 9hud, chain A (#38) with 8pi2, chain A (#35), sequence alignment
score = 1753.4
RMSD between 220 pruned atom pairs is 0.913 angstroms; (across all 331 pairs:
6.169)
> hide #!38 models
> show #!38 models
> hide #35 models
> show #35 models
> hide #35 models
> show #35 models
> hide #35 models
> hide #!38 models
> hide #!47 models
> show #!59 models
> open cryosparc_P483_J70_00018_volume_series vseries true
'cryosparc_P483_J70_00018_volume_series' has no suffix
> open
> /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_00_00018_volume.mrc
> /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_01_00018_volume.mrc
> /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_02_00018_volume.mrc
> /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_03_00018_volume.mrc
> /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_04_00018_volume.mrc
> /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_05_00018_volume.mrc
> /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_06_00018_volume.mrc
> /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_07_00018_volume.mrc
> /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_08_00018_volume.mrc
> /Users/amy/Desktop/cryosparc_P483_J70_00018_volume_series/J70_class_09_00018_volume.mrc
Opened J70_class_00_00018_volume.mrc as #60.1, grid size 64,64,64, pixel 4.52,
shown at level 0.113, step 1, values float32
Opened J70_class_01_00018_volume.mrc as #60.2, grid size 64,64,64, pixel 4.52,
shown at level 0.104, step 1, values float32
Opened J70_class_02_00018_volume.mrc as #60.3, grid size 64,64,64, pixel 4.52,
shown at level 0.109, step 1, values float32
Opened J70_class_03_00018_volume.mrc as #60.4, grid size 64,64,64, pixel 4.52,
shown at level 0.116, step 1, values float32
Opened J70_class_04_00018_volume.mrc as #60.5, grid size 64,64,64, pixel 4.52,
shown at level 0.106, step 1, values float32
Opened J70_class_05_00018_volume.mrc as #60.6, grid size 64,64,64, pixel 4.52,
shown at level 0.106, step 1, values float32
Opened J70_class_06_00018_volume.mrc as #60.7, grid size 64,64,64, pixel 4.52,
shown at level 0.116, step 1, values float32
Opened J70_class_07_00018_volume.mrc as #60.8, grid size 64,64,64, pixel 4.52,
shown at level 0.109, step 1, values float32
Opened J70_class_08_00018_volume.mrc as #60.9, grid size 64,64,64, pixel 4.52,
shown at level 0.106, step 1, values float32
Opened J70_class_09_00018_volume.mrc as #60.10, grid size 64,64,64, pixel
4.52, shown at level 0.113, step 1, values float32
> hide #!59 models
> surface dust #60.1 size 45.2
> surface dust #60.2 size 45.2
> surface dust #60.3 size 45.2
> surface dust #60.4 size 45.2
> surface dust #60.5 size 45.2
> surface dust #60.6 size 45.2
> surface dust #60.7 size 45.2
> surface dust #60.8 size 45.2
> surface dust #60.9 size 45.2
> surface dust #60.10 size 45.2
> hide #!60.1 models
> hide #!60.2 models
> hide #!60.3 models
> hide #!60.4 models
> hide #!60.5 models
> hide #!60.6 models
> hide #!60.7 models
> hide #!60.8 models
> hide #!60.9 models
> hide #!60.10 models
> show #!60.1 models
> show #!60.2 models
> hide #!60.1 models
> hide #!60.2 models
> show #!60.3 models
> show #!60.2 models
> hide #!60.2 models
> show #!60.4 models
> hide #!60.3 models
> show #!60.5 models
> hide #!60.4 models
> show #!60.6 models
> hide #!60.5 models
> show #!60.7 models
> hide #!60.6 models
> show #!60.8 models
> hide #!60.7 models
> show #!60.9 models
> hide #!60.8 models
> show #!60.10 models
> hide #!60.9 models
> hide #!60 target m
[Repeated 1 time(s)]
> close #60
> open
> /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_00_00020_volume.mrc
> /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_01_00020_volume.mrc
> /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_02_00020_volume.mrc
> /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_03_00020_volume.mrc
> /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_04_00020_volume.mrc
> /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_05_00020_volume.mrc
> /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_06_00020_volume.mrc
> /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_07_00020_volume.mrc
> /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_08_00020_volume.mrc
> /Users/amy/Downloads/cryosparc_P483_J124_00020_volume_series/J124_class_09_00020_volume.mrc
Opened J124_class_00_00020_volume.mrc as #60.1, grid size 64,64,64, pixel
4.52, shown at level 0.058, step 1, values float32
Opened J124_class_01_00020_volume.mrc as #60.2, grid size 64,64,64, pixel
4.52, shown at level 0.0583, step 1, values float32
Opened J124_class_02_00020_volume.mrc as #60.3, grid size 64,64,64, pixel
4.52, shown at level 0.0581, step 1, values float32
Opened J124_class_03_00020_volume.mrc as #60.4, grid size 64,64,64, pixel
4.52, shown at level 0.0576, step 1, values float32
Opened J124_class_04_00020_volume.mrc as #60.5, grid size 64,64,64, pixel
4.52, shown at level 0.0607, step 1, values float32
Opened J124_class_05_00020_volume.mrc as #60.6, grid size 64,64,64, pixel
4.52, shown at level 0.0608, step 1, values float32
Opened J124_class_06_00020_volume.mrc as #60.7, grid size 64,64,64, pixel
4.52, shown at level 0.0585, step 1, values float32
Opened J124_class_07_00020_volume.mrc as #60.8, grid size 64,64,64, pixel
4.52, shown at level 0.0573, step 1, values float32
Opened J124_class_08_00020_volume.mrc as #60.9, grid size 64,64,64, pixel
4.52, shown at level 0.0591, step 1, values float32
Opened J124_class_09_00020_volume.mrc as #60.10, grid size 64,64,64, pixel
4.52, shown at level 0.0602, step 1, values float32
> surface dust #60.1 size 45.2
> surface dust #60.2 size 45.2
> surface dust #60.3 size 45.2
> surface dust #60.4 size 45.2
> surface dust #60.5 size 45.2
> surface dust #60.6 size 45.2
> surface dust #60.7 size 45.2
> surface dust #60.8 size 45.2
> surface dust #60.9 size 45.2
> surface dust #60.10 size 45.2
> hide #!60 models
> show #!60 models
> hide #!60.1 models
> hide #!60.2 models
> hide #!60.3 models
> hide #!60.4 models
> hide #!60.5 models
> hide #!60.6 models
> hide #!60.7 models
> hide #!60.8 models
> hide #!60.9 models
> hide #!60.10 models
> show #!60.1 models
> show #!60.2 models
> hide #!60.1 models
> show #!60.3 models
> hide #!60.2 models
> show #!60.4 models
> hide #!60.3 models
> show #!60.5 models
> hide #!60.4 models
> show #!60.6 models
> hide #!60.5 models
> show #!60.7 models
> hide #!60.6 models
> show #!60.8 models
> hide #!60.7 models
> show #!60.9 models
> hide #!60.8 models
> show #!60.10 models
> hide #!60.9 models
> hide #!60.10 models
> open /Users/amy/Downloads/cryosparc_P483_J131_007_volume_map.mrc
Opened cryosparc_P483_J131_007_volume_map.mrc as #61, grid size 400,400,400,
pixel 0.723, shown at level 0.00743, step 2, values float32
> volume #61 level 0.0358
> transparency #61 50
Cell requested for row 59 is out of bounds for table with 71 rows! Resizing
table model.
> close #60
> show #!57 models
> hide #!57 models
> show #!38 models
> select add #38
6282 atoms, 6138 bonds, 1077 residues, 1 model selected
> view matrix models
> #38,0.28938,-0.95095,0.1093,139.21,-0.034645,0.10371,0.994,138.64,-0.95659,-0.29143,-0.0029341,290.92
> view matrix models
> #38,-0.45918,-0.73297,0.50191,244.33,0.66345,0.092766,0.74245,31.785,-0.59075,0.67391,0.44369,190.43
> view matrix models
> #38,-0.45918,-0.73297,0.50191,252.99,0.66345,0.092766,0.74245,27.709,-0.59075,0.67391,0.44369,215.88
> view matrix models
> #38,-0.45918,-0.73297,0.50191,245.4,0.66345,0.092766,0.74245,38.203,-0.59075,0.67391,0.44369,230.11
> view matrix models
> #38,0.7804,-0.38868,0.4898,36.281,-0.57699,-0.14577,0.80364,242.79,-0.24096,-0.90977,-0.33802,245.32
> view matrix models
> #38,0.24076,-0.088229,0.96657,104.14,-0.7449,-0.65522,0.12574,297.37,0.62222,-0.75027,-0.22348,101.24
> view matrix models
> #38,0.24076,-0.088229,0.96657,102.45,-0.7449,-0.65522,0.12574,304,0.62222,-0.75027,-0.22348,88.677
> volume flip #61 axis z
Opened cryosparc_P483_J131_007_volume_map.mrc z flip as #60, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> view matrix models
> #38,0.24076,-0.088229,0.96657,101.92,-0.7449,-0.65522,0.12574,291.88,0.62222,-0.75027,-0.22348,62.156
> view matrix models
> #38,0.44059,0.20906,0.87303,60.073,-0.32965,-0.86689,0.37395,231.22,0.83499,-0.45255,-0.31303,18.198
> view matrix models
> #38,0.44059,0.20906,0.87303,63.215,-0.32965,-0.86689,0.37395,234.58,0.83499,-0.45255,-0.31303,17.855
> fitmap #38 inMap #61
Fit molecule 9hud (#38) to map cryosparc_P483_J131_007_volume_map.mrc (#61)
using 6282 atoms
average map value = 0.03062, steps = 228
shifted from previous position = 12.1
rotated from previous position = 10.2 degrees
atoms outside contour = 4063, contour level = 0.0358
Position of 9hud (#38) relative to cryosparc_P483_J131_007_volume_map.mrc
(#61) coordinates:
Matrix rotation and translation
0.47633594 0.18597339 0.85937068 60.19776260
-0.46622754 -0.77523836 0.42618936 248.08769926
0.74547700 -0.60367159 -0.28256798 49.22817896
Axis -0.84117201 0.09302633 -0.53270606
Axis point 0.00000000 131.55393794 -45.87457813
Rotation angle (degrees) 142.25427000
Shift along axis -53.78213480
> fitmap #38 inMap #60
Fit molecule 9hud (#38) to map cryosparc_P483_J131_007_volume_map.mrc z flip
(#60) using 6282 atoms
average map value = 0.07254, steps = 164
shifted from previous position = 12.4
rotated from previous position = 8.44 degrees
atoms outside contour = 1769, contour level = 0.0358
Position of 9hud (#38) relative to cryosparc_P483_J131_007_volume_map.mrc z
flip (#60) coordinates:
Matrix rotation and translation
0.48808324 0.07900810 0.86921371 58.92380628
-0.57432345 -0.72083004 0.38801627 263.44883633
0.65721178 -0.68859406 -0.30644886 54.98864316
Axis -0.84303960 0.16600809 -0.51159120
Axis point 0.00000000 145.56353638 -47.97475612
Rotation angle (degrees) 140.31778784
Shift along axis -34.07217072
> show #!37 models
> mmaker #37 to #38
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 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
score = 1674.4
RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
0.519)
> open /Users/amy/Downloads/cryosparc_P483_J128_006_volume_map.mrc
Opened cryosparc_P483_J128_006_volume_map.mrc as #62, grid size 400,400,400,
pixel 0.723, shown at level 0.00501, step 2, values float32
> select subtract #38
Nothing selected
> hide #!38 models
> hide #!37 models
> hide #!60 models
> hide #!62 models
> open /Users/amy/Downloads/cryosparc_P483_J137_003_volume_map.mrc
Opened cryosparc_P483_J137_003_volume_map.mrc as #63, grid size 400,400,400,
pixel 0.723, shown at level 0.00802, step 2, values float32
> volume #63 level 0.03618
> volume flip #63 axis z
Opened cryosparc_P483_J137_003_volume_map.mrc z flip as #64, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> transparency #63 50
> transparency #64 50
> show #!38 models
> select add #38
6282 atoms, 6138 bonds, 1077 residues, 1 model selected
> show #!63 models
> hide #!64 models
> view matrix models
> #38,0.48808,0.079008,0.86921,57.589,-0.57432,-0.72083,0.38802,273.61,0.65721,-0.68859,-0.30645,79.373
> view matrix models
> #38,0.2297,0.46473,0.85514,83.832,-0.58104,-0.6394,0.50355,270.11,0.78079,-0.61253,0.12316,51.538
> view matrix models
> #38,0.2297,0.46473,0.85514,85.324,-0.58104,-0.6394,0.50355,273.24,0.78079,-0.61253,0.12316,53.863
> view matrix models
> #38,0.39662,0.46965,0.78875,59.564,-0.57284,-0.54478,0.61243,266.95,0.71732,-0.69472,0.052964,67.932
> show #!64 models
> hide #!63 models
> view matrix models
> #38,-0.91348,-0.3347,0.23136,304.61,0.38224,-0.51103,0.7699,112.62,-0.13945,0.79172,0.59475,139.64
> view matrix models
> #38,-0.59049,-0.80568,-0.046958,275.08,-0.087884,0.0063535,0.99611,164.3,-0.80225,0.59232,-0.074558,260.49
> view matrix models
> #38,-0.59049,-0.80568,-0.046958,273.4,-0.087884,0.0063535,0.99611,163.84,-0.80225,0.59232,-0.074558,241.17
> view matrix models
> #38,-0.55648,-0.77337,0.3037,262.39,0.12542,0.28314,0.95084,120.04,-0.82134,0.56721,-0.060566,244.98
> fitmap #38 inMap #64
Fit molecule 9hud (#38) to map cryosparc_P483_J137_003_volume_map.mrc z flip
(#64) using 6282 atoms
average map value = 0.03426, steps = 96
shifted from previous position = 4.73
rotated from previous position = 4.41 degrees
atoms outside contour = 3712, contour level = 0.036179
Position of 9hud (#38) relative to cryosparc_P483_J137_003_volume_map.mrc z
flip (#64) coordinates:
Matrix rotation and translation
-0.57799196 -0.77115445 0.26691966 270.23868060
0.05229306 0.29141704 0.95516572 129.97421192
-0.81436523 0.56603615 -0.12811068 246.02921542
Axis -0.27524806 0.76483926 0.58245980
Axis point 198.55971177 0.00000000 -12.15810570
Rotation angle (degrees) 135.01912752
Shift along axis 168.32883368
> hide #!64 models
> show #!63 models
> view matrix models
> #38,0.28227,0.88622,0.36734,69.32,0.13351,-0.41547,0.89976,144.95,0.95,-0.20493,-0.23559,-2.1095
> view matrix models
> #38,0.28227,0.88622,0.36734,65.915,0.13351,-0.41547,0.89976,149,0.95,-0.20493,-0.23559,14.639
> view matrix models
> #38,-0.00068529,0.90537,0.42463,109.22,-0.0059164,-0.42462,0.90535,171.33,0.99998,-0.0018918,0.0056475,-4.0739
> fitmap #38 inMap #63
Fit molecule 9hud (#38) to map cryosparc_P483_J137_003_volume_map.mrc (#63)
using 6282 atoms
average map value = 0.03246, steps = 440
shifted from previous position = 6.15
rotated from previous position = 34.9 degrees
atoms outside contour = 3887, contour level = 0.036179
Position of 9hud (#38) relative to cryosparc_P483_J137_003_volume_map.mrc
(#63) coordinates:
Matrix rotation and translation
0.42909681 0.75362179 0.49792584 49.09248009
-0.38069938 -0.34900840 0.85630668 221.91213193
0.81911167 -0.55699852 0.13714496 46.28691655
Axis -0.76791055 -0.17451431 -0.61632632
Axis point -0.00000000 97.45467483 -84.23279059
Rotation angle (degrees) 113.04060047
Shift along axis -104.95332191
> hide #!63 models
> show #!64 models
> view matrix models
> #38,0.6404,-0.29362,0.70969,53.209,-0.098072,0.88521,0.45474,134.87,-0.76175,-0.36082,0.5381,283.79
> view matrix models
> #38,-0.26615,-0.29672,0.91713,194.12,0.6919,0.60364,0.39609,21.458,-0.67114,0.73998,0.044637,233.39
> view matrix models
> #38,0.42821,0.78395,0.44952,48.675,0.43344,0.2583,-0.86337,91.334,-0.79295,0.56454,-0.22919,262.81
> view matrix models
> #38,0.40387,0.68567,-0.6056,69.485,-0.40554,-0.4592,-0.79036,250.65,-0.82002,0.5648,0.092606,263.06
> view matrix models
> #38,-0.85722,-0.30291,-0.41645,304.52,-0.2744,-0.41565,0.86714,207.52,-0.43576,0.8576,0.27319,188.79
> view matrix models
> #38,-0.57679,-0.55417,0.60017,257.1,0.51884,0.31896,0.79314,54.792,-0.63097,0.76887,0.10355,225.19
> view matrix models
> #38,-0.57679,-0.55417,0.60017,254.28,0.51884,0.31896,0.79314,61.36,-0.63097,0.76887,0.10355,204.28
> view matrix models
> #38,-0.60566,-0.70889,0.36146,267.77,0.21101,0.29491,0.93193,109.24,-0.76724,0.64071,-0.029033,232.41
> view matrix models
> #38,-0.60566,-0.70889,0.36146,266.58,0.21101,0.29491,0.93193,105.92,-0.76724,0.64071,-0.029033,230.06
> view matrix models
> #38,-0.72224,-0.67174,0.16473,286.05,0.065572,0.1706,0.98316,133.05,-0.68853,0.72087,-0.079168,215.16
> view matrix models
> #38,-0.47003,-0.67432,0.56953,241.2,0.17784,0.55967,0.80941,102.54,-0.86455,0.48173,-0.14315,252.98
> view matrix models
> #38,-0.47003,-0.67432,0.56953,249.14,0.17784,0.55967,0.80941,98.999,-0.86455,0.48173,-0.14315,251.53
> view matrix models
> #38,-0.59825,-0.70633,0.37841,273.04,0.21367,0.31452,0.92489,101.29,-0.77229,0.63417,-0.037243,229.77
> fitmap #38 inMap #64
Fit molecule 9hud (#38) to map cryosparc_P483_J137_003_volume_map.mrc z flip
(#64) using 6282 atoms
average map value = 0.03512, steps = 80
shifted from previous position = 5.4
rotated from previous position = 3.39 degrees
atoms outside contour = 3664, contour level = 0.036179
Position of 9hud (#38) relative to cryosparc_P483_J137_003_volume_map.mrc z
flip (#64) coordinates:
Matrix rotation and translation
-0.63147092 -0.69242738 0.34898254 278.13803163
0.16768307 0.31747267 0.93332391 107.28593241
-0.75705144 0.64788536 -0.08436641 232.43243148
Axis -0.19962317 0.77351156 0.60152345
Axis point 188.76264795 0.00000000 -10.22905426
Rotation angle (degrees) 134.36143880
Shift along axis 167.27766991
> fitmap #38 inMap #64
Fit molecule 9hud (#38) to map cryosparc_P483_J137_003_volume_map.mrc z flip
(#64) using 6282 atoms
average map value = 0.03512, steps = 40
shifted from previous position = 0.0099
rotated from previous position = 0.0115 degrees
atoms outside contour = 3662, contour level = 0.036179
Position of 9hud (#38) relative to cryosparc_P483_J137_003_volume_map.mrc z
flip (#64) coordinates:
Matrix rotation and translation
-0.63136485 -0.69247722 0.34907556 278.12932035
0.16783951 0.31744825 0.93330409 107.26947039
-0.75710524 0.64784406 -0.08420063 232.43949274
Axis -0.19960443 0.77348336 0.60156592
Axis point 188.76447494 0.00000000 -10.24425096
Rotation angle (degrees) 134.35152473
Shift along axis 167.28298509
> view matrix models
> #38,-0.63136,-0.69248,0.34908,274.79,0.16784,0.31745,0.9333,108.96,-0.75711,0.64784,-0.084201,230.09
> fitmap #38 inMap #64
Fit molecule 9hud (#38) to map cryosparc_P483_J137_003_volume_map.mrc z flip
(#64) using 6282 atoms
average map value = 0.03512, steps = 88
shifted from previous position = 4.42
rotated from previous position = 0.00894 degrees
atoms outside contour = 3663, contour level = 0.036179
Position of 9hud (#38) relative to cryosparc_P483_J137_003_volume_map.mrc z
flip (#64) coordinates:
Matrix rotation and translation
-0.63139892 -0.69244150 0.34908479 278.12602696
0.16773664 0.31755383 0.93328667 107.27376736
-0.75709963 0.64783049 -0.08435534 232.44361126
Axis -0.19961308 0.77352989 0.60150323
Axis point 188.76295474 0.00000000 -10.22421164
Rotation angle (degrees) 134.35485805
Shift along axis 167.27745334
> view matrix models
> #38,-0.64713,-0.6735,0.35724,279.79,0.16615,0.33274,0.92827,107.01,-0.74406,0.66006,-0.10342,230.15
> view matrix models
> #38,-0.64713,-0.6735,0.35724,276.58,0.16615,0.33274,0.92827,108.12,-0.74406,0.66006,-0.10342,229.13
> fitmap #38 inMap #64
Fit molecule 9hud (#38) to map cryosparc_P483_J137_003_volume_map.mrc z flip
(#64) using 6282 atoms
average map value = 0.03512, steps = 80
shifted from previous position = 3.52
rotated from previous position = 1.63 degrees
atoms outside contour = 3659, contour level = 0.036179
Position of 9hud (#38) relative to cryosparc_P483_J137_003_volume_map.mrc z
flip (#64) coordinates:
Matrix rotation and translation
-0.63138477 -0.69243824 0.34911684 278.12114525
0.16772204 0.31760740 0.93327106 107.27149167
-0.75711466 0.64780772 -0.08439532 232.44867407
Axis -0.19961431 0.77354815 0.60147934
Axis point 188.76284344 0.00000000 -10.21708948
Rotation angle (degrees) 134.35374707
Shift along axis 167.27577632
> hide #!64 models
> show #!60 models
> view matrix models
> #38,0.4887,0.003934,0.87244,67.696,-0.61017,-0.71321,0.345,277.22,0.6236,-0.70094,-0.34614,69.091
> view matrix models
> #38,0.4887,0.003934,0.87244,62.759,-0.61017,-0.71321,0.345,271.12,0.6236,-0.70094,-0.34614,59.706
> view matrix models
> #38,0.4887,0.003934,0.87244,62.878,-0.61017,-0.71321,0.345,270.83,0.6236,-0.70094,-0.34614,60.391
> select subtract #38
Nothing selected
> hide #!38 models
> show #!38 models
> open /Users/amy/Downloads/cryosparc_P483_J136_004_volume_map.mrc
Opened cryosparc_P483_J136_004_volume_map.mrc as #65, grid size 400,400,400,
pixel 0.723, shown at level 0.00461, step 2, values float32
> hide #!60 models
> hide #!38 models
> surface dust #65 size 7.23
> volume #65 level 0.02522
> transparency #65 50
> volume flip #65 axis z
Opened cryosparc_P483_J136_004_volume_map.mrc z flip as #66, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> show #!38 models
> fitmap #38 inMap #66
Fit molecule 9hud (#38) to map cryosparc_P483_J136_004_volume_map.mrc z flip
(#66) using 6282 atoms
average map value = 0.05359, steps = 80
shifted from previous position = 1.58
rotated from previous position = 4.51 degrees
atoms outside contour = 1373, contour level = 0.025222
Position of 9hud (#38) relative to cryosparc_P483_J136_004_volume_map.mrc z
flip (#66) coordinates:
Matrix rotation and translation
0.49152778 0.08078197 0.86710711 58.94196264
-0.57115257 -0.72173556 0.39100196 263.45649346
0.65740794 -0.68743877 -0.30861424 55.13461431
Axis -0.84417530 0.16414704 -0.51031737
Axis point 0.00000000 145.46690985 -47.79590518
Rotation angle (degrees) 140.30102750
Shift along axis -34.64789549
> mmaker #37 to #38
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 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
score = 1674.4
RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
0.519)
> show #!37 models
> show #7 models
> mmaker #7 to #37
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 1ezx, chain C (#37) with 5a0c, chain A (#7), sequence alignment
score = 241.2
RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
3.073)
> hide #!37 models
> show #!37 models
> hide #!38 models
> show #!38 models
> hide #!37 models
> show #!37 models
> hide #!38 models
> hide #7 models
> volume #65 level 0.03378
> volume #66 level 0.03927
> volume #66 level 0.03004
> hide #!37 models
> volume gaussian #65 sDev 2
Opened cryosparc_P483_J136_004_volume_map.mrc gaussian as #67, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> ui tool show "Segment Map"
Segmenting cryosparc_P483_J136_004_volume_map.mrc gaussian, density threshold
0.002595
Only showing 60 of 69 regions.
Showing 60 of 69 region surfaces
165 watershed regions, grouped to 69 regions
Showing cryosparc_P483_J136_004_volume_map gaussian.seg - 69 regions, 60
surfaces
> select #68.13
1 model selected
> select add #68.6
2 models selected
> select add #68.23
3 models selected
> select add #68.24
4 models selected
> select add #68.29
5 models selected
> select add #68.20
6 models selected
> select add #68.5
7 models selected
> select add #68.37
8 models selected
> select add #68.33
9 models selected
> select add #68.11
10 models selected
> select add #68.26
11 models selected
> select add #68.14
12 models selected
> select add #68.7
13 models selected
> select add #68.3
14 models selected
> select add #68.19
15 models selected
> select add #68.8
16 models selected
> select add #68.35
17 models selected
> select add #68.28
18 models selected
> select add #68.12
19 models selected
> select add #68.15
20 models selected
> select add #68.4
21 models selected
> select add #68.40
22 models selected
> select add #68.36
23 models selected
> select add #68.48
24 models selected
> select add #68.51
25 models selected
> select add #68.53
26 models selected
> select add #68.59
27 models selected
> select add #68.58
28 models selected
> select add #68.57
29 models selected
> select add #68.54
30 models selected
> select add #68.16
31 models selected
> select add #68.44
32 models selected
> select add #68.25
33 models selected
> select add #68.50
34 models selected
> select add #68.31
35 models selected
> hide #!67 models
> select add #68.45
36 models selected
> select add #68.38
37 models selected
> select add #68.17
38 models selected
> select add #68.34
39 models selected
> select add #68.52
40 models selected
> select add #68.30
41 models selected
> select add #68.27
42 models selected
> select add #68.49
43 models selected
> select add #68.46
44 models selected
> select add #68.43
45 models selected
> select add #68.39
46 models selected
> select add #68.41
47 models selected
> select add #68.56
48 models selected
> select add #68.55
49 models selected
> show #!67 models
> show #!66 models
> hide #!66 models
> hide #!68 models
> show #!68 models
> hide #!68 models
> show #!66 models
> show #!68 models
> hide #!67 models
> hide #!66 models
> show #!65 models
> select add #68.42
50 models selected
> hide #!65 models
> select add #68.21
51 models selected
> show #!66 models
> hide #!66 models
> show #!65 models
> hide #!68 models
> show #!68 models
> hide #!68 models
> show #!68 models
> select add #68.47
52 models selected
> select add #68.10
53 models selected
> select subtract #68.10
52 models selected
> select add #68.60
53 models selected
> select add #68.1
54 models selected
> select subtract #68.1
53 models selected
> select add #68.1
54 models selected
> select subtract #68.1
53 models selected
> select #68.1
1 model selected
Segmenting cryosparc_P483_J136_004_volume_map.mrc gaussian, density threshold
0.002595
Only showing 60 of 69 regions.
Showing 60 of 69 region surfaces
165 watershed regions, grouped to 69 regions
Showing cryosparc_P483_J136_004_volume_map gaussian.seg - 69 regions, 60
surfaces
> close #68
> show #!67 models
> hide #!67 models
> volume #65 level 0.009704
> ui mousemode right "map eraser"
> volume erase #65 center 171.23,100.86,184.61 radius 29.508
Opened cryosparc_P483_J136_004_volume_map.mrc copy as #69, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> volume erase #69 center 84.398,121.62,173.8 radius 29.498
> surface dust #69 size 7.23
> volume #69 level 0.01365
> volume #69 level 0.01523
> ui mousemode right "translate selected models"
> volume gaussian #65 sDev 2
Opened cryosparc_P483_J136_004_volume_map.mrc gaussian as #68, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> ui mousemode right "map eraser"
Can only have one displayed volume when erasing
> hide #!69 models
> show #!69 models
> hide #!69 models
> hide #!68 models
> show #!68 models
> volume erase #68 center 199.87,114.16,177.51 radius 29.932
> volume erase #68 center 223.51,161,191.94 radius 29.932
> volume erase #68 center 230.79,129.47,140.96 radius 29.932
> volume erase #68 center 137.16,147.6,54.19 radius 29.932
> volume erase #68 center 74.443,93.395,201.66 radius 29.932
> volume erase #68 center 60.662,109.56,169.96 radius 29.932
> volume erase #68 center 81.784,129.86,147.37 radius 29.932
> volume erase #68 center 97.833,142.74,184.92 radius 14.894
> volume erase #68 center 93.234,158.27,115.41 radius 14.894
> volume erase #68 center 110.51,164.91,187.37 radius 14.894
> volume erase #68 center 126.3,181.61,190.42 radius 14.894
> volume erase #68 center 190.02,108.44,206.29 radius 14.894
> volume erase #68 center 212,136.35,210.5 radius 14.894
> volume erase #68 center 66.419,147.34,177.91 radius 14.894
> volume erase #68 center 94.954,148.62,156.51 radius 14.894
> volume erase #68 center 105.75,136.11,158.02 radius 14.894
> volume erase #68 center 169.12,113.8,156.36 radius 12.58
> volume erase #68 center 179.1,115.64,198.32 radius 12.58
> show #!65 models
> hide #!68 models
> volume #65 level 0.01773
> show #!68 models
Can only have one displayed volume when erasing
> hide #!65 models
> hide #!68 models
> show #!65 models
> hide #!65 models
> show #!68 models
> volume erase #68 center 173.45,108.86,188.42 radius 22.124
> volume erase #68 center 161.71,101.56,178.92 radius 22.124
> undo
[Repeated 1 time(s)]
> show #!68 models
> hide #!65 models
> volume erase #68 center 92.336,122.06,161.51 radius 22.124
Segmenting cryosparc_P483_J136_004_volume_map.mrc gaussian, density threshold
0.002595
Showing 50 region surfaces
124 watershed regions, grouped to 50 regions
Showing cryosparc_P483_J136_004_volume_map gaussian.seg - 50 regions, 50
surfaces
> select add #70.10
1 model selected
> select add #70.31
2 models selected
> select add #70.6
3 models selected
> select add #70.12
4 models selected
> select add #70.23
5 models selected
> select add #70.22
6 models selected
Drag select of 173, 7505 of 52828 triangles, 177, 26288 of 45472 triangles,
172, 156, 176, 25800 of 38068 triangles, 157, 17988 of 30408 triangles, 167,
152, 142, 6687 of 22324 triangles, 163, 64, 17140 of 19708 triangles, 12, 178,
169, 568 of 17388 triangles, 5, 143, 6044 of 15344 triangles, 144, 148, 135,
30, 12770 of 12984 triangles, 8, 52, 4331 of 12948 triangles, 125, 11085 of
12828 triangles, 6, 68, 5141 of 9284 triangles, 33, 35, 6919 of 6948
triangles, 68 cryosparc_P483_J136_004_volume_map.mrc gaussian
Drag select of 177, 8907 of 45472 triangles, 172, 35825 of 37284 triangles,
156, 176, 5888 of 38068 triangles, 157, 7846 of 30408 triangles, 167, 152,
7570 of 25900 triangles, 163, 12, 17106 of 17656 triangles, 178, 5, 144, 148,
13560 of 13800 triangles, 135, 12555 of 14540 triangles, 30, 6391 of 12984
triangles, 8, 125, 1329 of 12828 triangles, 6, 33, 3490 of 7340 triangles, 35,
1963 of 6948 triangles, 68 cryosparc_P483_J136_004_volume_map.mrc gaussian
> hide #!68 models
Drag select of 177, 10859 of 45472 triangles, 172, 176, 10027 of 38068
triangles, 149, 177 of 29032 triangles, 152, 12625 of 25900 triangles, 163, 5,
144, 135, 14423 of 14540 triangles, 30, 11045 of 12984 triangles, 8, 125, 2434
of 12828 triangles, 6, 33, 6568 of 7340 triangles, 35, 5541 of 6948 triangles
> close #70
> show #!66 models
> hide #!66 models
> show #!65 models
> show #!68 models
> close #68-69
> close #67
> volume gaussian #65 sDev 2
Opened cryosparc_P483_J136_004_volume_map.mrc gaussian as #67, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> open /Users/amy/Downloads/cryosparc_P371_J1247_003_volume_map.mrc
Opened cryosparc_P371_J1247_003_volume_map.mrc as #68, grid size 300,300,300,
pixel 0.867, shown at level 0.0217, step 2, values float32
> hide #!67 models
> volume #68 level 0.07077
> show #!8 models
> transparenct #68 50
Unknown command: transparenct #68 50
> transparency #68 50
> fitmap #8 inMap #68
Fit molecule 1ezx (#8) to map cryosparc_P371_J1247_003_volume_map.mrc (#68)
using 3984 atoms
average map value = 0.0799, steps = 64
shifted from previous position = 1.9
rotated from previous position = 5.61 degrees
atoms outside contour = 1925, contour level = 0.07077
Position of 1ezx (#8) relative to cryosparc_P371_J1247_003_volume_map.mrc
(#68) coordinates:
Matrix rotation and translation
-0.34797185 0.02707514 -0.93711394 206.68051797
0.14066384 -0.98675962 -0.08074121 177.03298135
-0.92689227 -0.15991372 0.33955607 198.02271581
Axis -0.57026324 -0.07362457 0.81815601
Axis point 168.54386706 102.19253410 0.00000000
Rotation angle (degrees) 176.01946831
Shift along axis 31.11719577
> show #!57 models
> select add #57
1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 3 models selected
> mmaker #57 to #8
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 1ezx, chain C (#8) with copy of 1ezx, chain C (#57), sequence
alignment score = 1096
RMSD between 140 pruned atom pairs is 0.000 angstroms; (across all 140 pairs:
0.000)
> select subtract #57
Nothing selected
> select add #57
1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 3 models selected
> hide #!8 models
> show #!8 models
> ui mousemode right "translate selected models"
> view matrix models
> #57,-0.55581,-0.066238,-0.82867,220.13,0.27617,-0.95492,-0.10891,166.76,-0.7841,-0.28938,0.54905,178.74
> view matrix models
> #57,-0.44814,0.013112,-0.89387,212.91,0.19695,-0.97388,-0.11303,173.83,-0.872,-0.2267,0.43385,190.3
> view matrix models
> #57,-0.44814,0.013112,-0.89387,212.84,0.19695,-0.97388,-0.11303,176.3,-0.872,-0.2267,0.43385,191.28
> view matrix models
> #57,-0.70986,-0.70171,-0.060879,208.01,0.69037,-0.67603,-0.25765,136.82,0.13964,-0.22492,0.96432,82.152
> view matrix models
> #57,-0.70986,-0.70171,-0.060879,209.15,0.69037,-0.67603,-0.25765,137.83,0.13964,-0.22492,0.96432,86.098
> view matrix models
> #57,-0.52828,-0.77583,-0.34499,210.69,0.84041,-0.53567,-0.082284,113.45,-0.12096,-0.3334,0.93499,111.22
> fitmap #57 inMap #68
Fit molecule copy of 1ezx (#57) to map cryosparc_P371_J1247_003_volume_map.mrc
(#68) using 1009 atoms
average map value = 0.05715, steps = 92
shifted from previous position = 1.85
rotated from previous position = 22.4 degrees
atoms outside contour = 740, contour level = 0.07077
Position of copy of 1ezx (#57) relative to
cryosparc_P371_J1247_003_volume_map.mrc (#68) coordinates:
Matrix rotation and translation
-0.60074737 -0.69741151 -0.39079378 215.40326299
0.67365936 -0.70482938 0.22225799 115.60603445
-0.43044821 -0.12974098 0.89324219 133.98043752
Axis -0.24857103 0.02800277 0.96820880
Axis point 100.60140928 106.25888332 0.00000000
Rotation angle (degrees) 134.92392438
Shift along axis 79.41531641
> hide #!8 models
> view matrix models
> #57,-0.55549,-0.80836,-0.19489,204.29,0.77301,-0.58839,0.23717,104.09,-0.30639,-0.018907,0.95172,118.37
> view matrix models
> #57,-0.55549,-0.80836,-0.19489,206,0.77301,-0.58839,0.23717,104.98,-0.30639,-0.018907,0.95172,120.21
> view matrix models
> #57,-0.33676,-0.93674,0.09544,176.41,0.94008,-0.34023,-0.022246,98.96,0.05331,0.08223,0.99519,86.499
> view matrix models
> #57,-0.33676,-0.93674,0.09544,176.42,0.94008,-0.34023,-0.022246,99.819,0.05331,0.08223,0.99519,85.597
> view matrix models
> #57,-0.11119,-0.60614,-0.78754,195.64,0.65285,-0.64203,0.40198,108.39,-0.74928,-0.46945,0.46711,190.42
> view matrix models
> #57,0.78168,0.24914,-0.57175,92.445,0.18825,-0.96824,-0.16454,182.56,-0.59459,0.020991,-0.80376,231.51
> view matrix models
> #57,0.51703,0.78986,-0.32985,88.973,0.65853,-0.61323,-0.43621,150.13,-0.54682,0.0083211,-0.83721,229.65
> view matrix models
> #57,0.51703,0.78986,-0.32985,91.831,0.65853,-0.61323,-0.43621,150.09,-0.54682,0.0083211,-0.83721,234.12
> view matrix models
> #57,0.55299,0.36331,-0.7498,120.29,0.22263,-0.93163,-0.28721,185.16,-0.80289,-0.0081052,-0.59607,242.91
> view matrix models
> #57,0.55299,0.36331,-0.7498,118.48,0.22263,-0.93163,-0.28721,185.69,-0.80289,-0.0081052,-0.59607,239.55
> view matrix models
> #57,0.92569,-0.35496,0.13079,59.902,0.0091285,-0.32469,-0.94578,222.6,0.37818,0.87669,-0.29732,108.08
> view matrix models
> #57,-0.3165,-0.83947,0.44172,155.86,0.42443,-0.54177,-0.7255,182.72,0.84834,-0.042141,0.52777,49.092
> view matrix models
> #57,-0.3165,-0.83947,0.44172,156.19,0.42443,-0.54177,-0.7255,182.46,0.84834,-0.042141,0.52777,49.883
> view matrix models
> #57,0.040165,-0.95688,0.2877,137.9,0.92992,-0.069542,-0.36112,111.92,0.36556,0.28204,0.88703,63.1
> view matrix models
> #57,0.040165,-0.95688,0.2877,138.99,0.92992,-0.069542,-0.36112,111.84,0.36556,0.28204,0.88703,64.867
> view matrix models
> #57,0.18721,-0.98102,0.050423,139.78,0.96897,0.17599,-0.17355,93.385,0.16139,0.081349,0.98353,81.124
> mmaker #7 to #8
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 1ezx, chain C (#8) with 5a0c, chain A (#7), sequence alignment
score = 241.2
RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
3.073)
> select add #7
2892 atoms, 2759 bonds, 5 pseudobonds, 549 residues, 4 models selected
> show #7 models
> select subtract #57
1883 atoms, 1745 bonds, 394 residues, 1 model selected
> hide #!57 models
> select #7/A
1883 atoms, 1745 bonds, 394 residues, 1 model selected
> select subtract #7
Nothing selected
> select #7/A
1883 atoms, 1745 bonds, 394 residues, 1 model selected
> select #7/A: 202
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #7/A: 202
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 6 atom styles
> rainbow sel
> select add #7
1883 atoms, 1745 bonds, 394 residues, 1 model selected
> select subtract #7
Nothing selected
> show #!37 models
> hide #!37 models
> show #!8 models
> hide #!8 models
> open /Users/amy/Downloads/cryosparc_P371_J1248_004_volume_map.mrc
Opened cryosparc_P371_J1248_004_volume_map.mrc as #69, grid size 300,300,300,
pixel 0.867, shown at level 0.0367, step 2, values float32
> volume #69 level 0.08383
> hide #!68 models
> volume #69 level 0.0762
> transparency #69 50
> hide #7 models
> close #50-56
> close #43-48
> show #!65 models
> volume gaussian #65 sDev 2
Opened cryosparc_P483_J136_004_volume_map.mrc gaussian as #43, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> ui mousemode right "map eraser"
> volume erase #43 center 75.013,107.83,176.28 radius 23.833
> volume erase #43 center 194.75,109.99,182.34 radius 28.983
> volume erase #43 center 224.93,121.74,145.38 radius 28.983
> volume erase #43 center 210.7,158.2,175.15 radius 28.983
> volume erase #43 center 208.21,147.09,205.7 radius 28.983
> volume erase #43 center 188.54,118.48,207.86 radius 28.983
> volume erase #43 center 76.857,145.76,159.87 radius 28.983
> volume erase #43 center 87.79,161.6,111.25 radius 28.983
> volume erase #43 center 126.19,148.22,60.086 radius 28.983
> surface dust #43 size 7.23
[Repeated 2 time(s)]
> volume erase #43 center 98.252,123.11,133.43 radius 28.983
> ui mousemode right "translate selected models"
> hide #!43 models
> show #!43 models
Segmenting cryosparc_P483_J136_004_volume_map.mrc gaussian, density threshold
0.002595
Showing 54 region surfaces
134 watershed regions, grouped to 54 regions
Showing cryosparc_P483_J136_004_volume_map gaussian.seg - 54 regions, 54
surfaces
Drag select of 180, 4556 of 45584 triangles, 187, 31245 of 37284 triangles,
177, 33991 of 34540 triangles, 179, 626 of 37968 triangles, 170, 1849 of 30408
triangles, 183, 146, 4014 of 25900 triangles, 166, 12, 182, 5, 151, 157, 9644
of 13800 triangles, 160, 7260 of 14540 triangles, 30, 3371 of 12984 triangles,
8, 6, 33, 892 of 7340 triangles, 35, 143 of 6948 triangles, 43
cryosparc_P483_J136_004_volume_map.mrc gaussian
Drag select of 189, 15171 of 45152 triangles, 144, 28176 of 29416 triangles,
186, 153, 26060 of 29032 triangles, 165, 16225 of 23204 triangles, 171, 20862
of 21324 triangles, 181, 612 of 19816 triangles, 188, 9417 of 18732 triangles,
184, 11190 of 17388 triangles, 69, 12493 of 16160 triangles, 83, 159, 3373 of
15344 triangles, 100, 109, 4788 of 13396 triangles, 54, 54 of 12948 triangles,
190, 3956 of 13608 triangles, 148, 93 of 11564 triangles, 167, 713 of 12312
triangles, 136, 1067 of 12828 triangles, 95, 7439 of 9752 triangles, 82, 43
cryosparc_P483_J136_004_volume_map.mrc gaussian
> hide #!43 models
> show #!43 models
> select add #44.51
41 models selected
> select add #44.53
42 models selected
> hide #!43 models
> select add #44.10
43 models selected
Ungrouped to 64 regions, but did not show all surfaces, see Options
> select clear
> select #44.62
1 model selected
> select #44.21
1 model selected
Ungrouped to 2 regions, but did not show their surfaces, see Options
Smoothing and grouping, standard deviation 5 voxels
Showing 28 region surfaces
Got 28 regions after smoothing 5 voxels.
Ungrouped to 86 regions, but did not show all surfaces, see Options
Drag select of 134
[Repeated 1 time(s)]
> select clear
> select #44.72
1 model selected
> select clear
> select #44.73
1 model selected
> select add #44.74
2 models selected
> show #!43 models
> hide #!44 models
> volume #43 level 0.01177
> ui mousemode right "map eraser"
> volume erase #43 center 170.19,107.1,177.93 radius 16.889
> ui mousemode right "translate selected models"
> close #44
> volume gaussian #65 sDev 2
Opened cryosparc_P483_J136_004_volume_map.mrc gaussian as #44, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> close #44
Segmenting cryosparc_P483_J136_004_volume_map.mrc gaussian, density threshold
0.011767
Showing 49 region surfaces
113 watershed regions, grouped to 49 regions
Showing cryosparc_P483_J136_004_volume_map gaussian.seg - 49 regions, 49
surfaces
> hide #!43 models
Drag select of 152, 22015 of 40248 triangles, 160, 137, 162, 19815 of 27632
triangles, 145, 22686 of 24068 triangles, 154, 132, 19102 of 20860 triangles,
149, 128, 343 of 19360 triangles, 12, 157, 151, 5666 of 14648 triangles, 155,
15 of 14140 triangles, 121, 8147 of 14452 triangles, 126, 124, 5, 50, 4342 of
11924 triangles, 6, 133, 26, 116, 11741 of 11768 triangles, 7, 32, 34
Drag select of 159, 9755 of 37648 triangles, 125, 24182 of 24328 triangles,
158, 18998 of 22744 triangles, 139, 10853 of 19468 triangles, 142, 17469 of
19372 triangles, 128, 5249 of 19360 triangles, 63, 3508 of 13216 triangles,
82, 11209 of 11804 triangles, 90, 161, 1720 of 12188 triangles, 84, 4555 of
9228 triangles, 71, 6615 of 6864 triangles
Drag select of 128, 163, 7108 of 17660 triangles, 94, 10211 of 10636
triangles, 123, 7213 of 10336 triangles, 146, 6495 of 11584 triangles, 88,
3550 of 8592 triangles
Showing 49 region surfaces
> select #44.46
1 model selected
> show #!43 models
> hide #!43 models
> select #44.13
1 model selected
> select #44.13
1 model selected
> select #44.3
1 model selected
> select #44.3
1 model selected
Ungrouped to 2 regions
> select #44.13
1 model selected
Ungrouped to 2 regions
> select #44.3
1 model selected
Ungrouped to 2 regions
> select #44.51
1 model selected
Ungrouped to 2 regions
> select #44.54
1 model selected
Ungrouped to 2 regions
> show #!43 models
> hide #!43 models
> show #!43 models
> hide #!43 models
> show #!43 models
> hide #!43 models
> select #44.55
1 model selected
> select #44.55
1 model selected
> select clear
Please select one ore more regions to save to .mrc file
Drag select of 156, 138, 61, 127, 65, 93, 87, 92, 76, 68, 79, 69
Saving 12 regions to mrc file...
Opened base_cryosparc_P483_J136_004_volume_map_12_regions.mrc as #45, grid
size 75,64,70, pixel 0.723, shown at step 1, values float32
Wrote base_cryosparc_P483_J136_004_volume_map_12_regions.mrc
> volume #45 level 0.01277
> hide #!44 models
> show #!44 models
Deleted 12 regions
Showing 42 region surfaces
> hide #!45 models
> show #!45 models
> hide #!45 models
Drag select of 152, 159, 160, 137, 162, 125, 158, 145, 154, 139, 132, 142,
149, 128, 163, 12, 157, 151, 155, 121, 126, 63, 82, 124, 5, 50, 6, 133, 90,
26, 161, 94, 116, 123, 146, 7, 84, 88, 74, 71, 32, 34
Saving 42 regions to mrc file...
Opened substract_cryosparc_P483_J136_004_volume_map_42_regions.mrc as #46,
grid size 90,89,178, pixel 0.723, shown at step 1, values float32
Wrote substract_cryosparc_P483_J136_004_volume_map_42_regions.mrc
> select add #44
43 models selected
> select subtract #44
Nothing selected
> hide #!44 models
> volume #46 level 0.01896
> show #!44 models
> hide #!44 models
> show #!45 models
> volume resample #45 onGrid #65
Opened base_cryosparc_P483_J136_004_volume_map_12_regions.mrc resampled as
#47, grid size 400,400,400, pixel 0.723, shown at step 1, values float32
> show #!45 models
> hide #!45 models
> volume resample #46 onGrid #65
Opened substract_cryosparc_P483_J136_004_volume_map_42_regions.mrc resampled
as #48, grid size 400,400,400, pixel 0.723, shown at step 1, values float32
> hide #!48 models
> show #!48 models
> save "/Users/amy/Desktop/SPA AAT_HNE/9C5_Fab_AAT_HNE/For mask
> generation/Base_mask_J136.mrc" models #47
> save "/Users/amy/Desktop/SPA AAT_HNE/9C5_Fab_AAT_HNE/For mask
> generation/Substract_mask_J136.mrc" models #48
> hide #!48 models
> hide #!47 models
> show #!66 models
> volume #66 level 0.01465
> hide #!66 models
> show #!66 models
> show #!65 models
> hide #!66 models
> hide #!65 models
> show #!66 models
> volume #66 level 0.0762
> volume #66 level 0.05963
> open /Users/amy/Downloads/Position_4_4_stack_Vol.mrc
Opened Position_4_4_stack_Vol.mrc as #50, grid size 1024,1024,200, pixel
6.2,6.2,6.2, shown at level 0.00197, step 4, values float32
> open /Users/amy/Downloads/cryosparc_P483_J163_009_volume_map.mrc
Opened cryosparc_P483_J163_009_volume_map.mrc as #51, grid size 400,400,400,
pixel 0.723, shown at level 0.00345, step 2, values float32
> hide #!50 models
> hide #!66 models
> close #50
> volume #51 level 0.01856
> transparency #51 50
> show #!38 models
> select add #38
6282 atoms, 6138 bonds, 1077 residues, 1 model selected
> volume flip #51 axis z
Opened cryosparc_P483_J163_009_volume_map.mrc z flip as #50, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> fitmap #38 inMap #50
Fit molecule 9hud (#38) to map cryosparc_P483_J163_009_volume_map.mrc z flip
(#50) using 6282 atoms
average map value = 0.07848, steps = 68
shifted from previous position = 0.869
rotated from previous position = 1.21 degrees
atoms outside contour = 1202, contour level = 0.018564
Position of 9hud (#38) relative to cryosparc_P483_J163_009_volume_map.mrc z
flip (#50) coordinates:
Matrix rotation and translation
0.47930263 0.06820977 0.87499511 60.65156876
-0.57459125 -0.72922061 0.37159415 263.89520826
0.66341081 -0.68087058 -0.31032461 53.93040141
Axis -0.84112622 0.16909745 -0.51372438
Axis point 0.00000000 145.65173307 -47.89349763
Rotation angle (degrees) 141.27168221
Shift along axis -34.09698023
> select subtract #38
Nothing selected
> show #!37 models
> mmaker #37 to #38
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 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
score = 1674.4
RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
0.519)
> hide #!37 models
> hide #!38 models
> show #!37 models
> ui mousemode right "tape measure"
> marker segment #52 position 174.9,170.7,80.95 toPosition 149.1,120.4,104.7
> color yellow radius 0.1807 label 61.39 labelHeight 6.139 labelColor yellow
> marker segment #52 position 173.6,172.2,80.09 toPosition 131.7,129.6,94.55
> color yellow radius 0.1807 label 61.46 labelHeight 6.146 labelColor yellow
> marker segment #52 position 168.9,170.1,79.92 toPosition 119.6,140.5,107.7
> color yellow radius 0.1807 label 63.85 labelHeight 6.385 labelColor yellow
> marker segment #52 position 162.3,169.9,78.45 toPosition 131.8,125.9,101.6
> color yellow radius 0.1807 label 58.29 labelHeight 5.829 labelColor yellow
> close #52
> open /Users/amy/Downloads/cryosparc_P483_J166_007_volume_map.mrc
Opened cryosparc_P483_J166_007_volume_map.mrc as #52, grid size 400,400,400,
pixel 0.723, shown at level 0.00871, step 2, values float32
> volume #52 level 0.03218
> volume flip #52 50
Expected a keyword
> volume flip #52 axis z
Opened cryosparc_P483_J166_007_volume_map.mrc z flip as #53, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> transparency #53 50
> fitmap #38 inMap #53
Fit molecule 9hud (#38) to map cryosparc_P483_J166_007_volume_map.mrc z flip
(#53) using 6282 atoms
average map value = 0.0755, steps = 88
shifted from previous position = 0.675
rotated from previous position = 2.29 degrees
atoms outside contour = 1730, contour level = 0.032179
Position of 9hud (#38) relative to cryosparc_P483_J166_007_volume_map.mrc z
flip (#53) coordinates:
Matrix rotation and translation
0.48708054 0.10074896 0.86752649 58.26714282
-0.57324776 -0.71251935 0.40460253 263.40109171
0.65889268 -0.69438163 -0.28930019 55.22725475
Axis -0.84150595 0.15975352 -0.51608774
Axis point 0.00000000 145.38448995 -49.65713741
Rotation angle (degrees) 139.23284387
Shift along axis -35.45500404
> show #!38 models
> mmaker #37 to #38
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 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
score = 1674.4
RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
0.519)
> hide #!38 models
> show #7 models
> mmaker #7 to #37
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 1ezx, chain C (#37) with 5a0c, chain A (#7), sequence alignment
score = 241.2
RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
3.073)
> hide #!37 models
> volume #53 level 0.09551
> volume #53 level 0.05065
> volume #53 level 0.04273
> hide #7 models
> open /Users/amy/Downloads/cryosparc_P483_J178_007_volume_map.mrc
Opened cryosparc_P483_J178_007_volume_map.mrc as #54, grid size 400,400,400,
pixel 0.723, shown at level 0.00984, step 2, values float32
> volume #54 level 0.02797
> volume flip #54 axis z
Opened cryosparc_P483_J178_007_volume_map.mrc z flip as #55, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> transparency #55 50
> show #7 models
> hide #7 models
> show #7 models
> select add #7
1883 atoms, 1745 bonds, 394 residues, 1 model selected
> select subtract #7
Nothing selected
> hide #7 models
> show #!8 models
> select add #8
3984 atoms, 3982 bonds, 5 pseudobonds, 592 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.74339,-0.4472,0.49738,176.11,0.56886,-0.81386,0.11846,127.4,0.35182,0.371,0.85941,53.336
> view matrix models
> #8,0.38457,0.070001,0.92044,48.03,0.66601,-0.71147,-0.22416,135.06,0.63917,0.69922,-0.32023,84.211
> view matrix models
> #8,0.38457,0.070001,0.92044,48.132,0.66601,-0.71147,-0.22416,145.94,0.63917,0.69922,-0.32023,107.63
> view matrix models
> #8,-0.11357,-0.011929,0.99346,82.463,0.67784,-0.73199,0.068701,129.45,0.72638,0.68121,0.091219,79.052
> hide #!55 models
> show #!54 models
> transparency #54 50
> view matrix models
> #8,-0.11357,-0.011929,0.99346,88.184,0.67784,-0.73199,0.068701,128.28,0.72638,0.68121,0.091219,43.943
> view matrix models
> #8,0.98922,0.13889,-0.046321,63.821,0.14063,-0.98938,0.036662,180.17,-0.040737,-0.042781,-0.99825,195.61
> view matrix models
> #8,-0.22454,0.34562,-0.91111,186.4,0.4892,-0.76865,-0.41214,170.57,-0.84277,-0.53826,0.0035149,218.83
> view matrix models
> #8,-0.22454,0.34562,-0.91111,190.27,0.4892,-0.76865,-0.41214,172.31,-0.84277,-0.53826,0.0035149,198.32
> hide #!8 models
> select subtract #8
Nothing selected
> show #!38 models
> select add #38
6282 atoms, 6138 bonds, 1077 residues, 1 model selected
> view matrix models
> #38,0.58456,0.63428,-0.50594,39.545,0.32988,0.3839,0.86244,72.759,0.74126,-0.67105,0.015176,37.498
> view matrix models
> #38,-0.62989,-0.2889,-0.72095,269.75,0.43669,0.63589,-0.63635,64.932,0.64229,-0.71567,-0.27439,58.484
> view matrix models
> #38,-0.79758,-0.56471,-0.21208,300.49,0.093917,0.23104,-0.9684,138.83,0.59586,-0.79229,-0.13123,66.978
> view matrix models
> #38,-0.79758,-0.56471,-0.21208,298.65,0.093917,0.23104,-0.9684,128.19,0.59586,-0.79229,-0.13123,84.027
> view matrix models
> #38,-0.65099,-0.75245,0.1001,278.77,-0.2865,0.12144,-0.95035,192.34,0.70294,-0.64735,-0.29463,63.572
> view matrix models
> #38,-0.65099,-0.75245,0.1001,273.74,-0.2865,0.12144,-0.95035,188.77,0.70294,-0.64735,-0.29463,64.627
> hide #!54 models
> show #!55 models
> view matrix models
> #38,0.92945,0.36602,-0.046307,-17.327,-0.12262,0.18809,-0.97447,160.6,-0.34796,0.9114,0.2197,164.6
> view matrix models
> #38,0.68418,0.72711,0.05661,6.3245,-0.24646,0.30357,-0.92038,175.08,-0.6864,0.61576,0.3869,227.39
> view matrix models
> #38,0.68418,0.72711,0.05661,6.2981,-0.24646,0.30357,-0.92038,173.03,-0.6864,0.61576,0.3869,222.11
> fitmap #38 inMap #55
Fit molecule 9hud (#38) to map cryosparc_P483_J178_007_volume_map.mrc z flip
(#55) using 6282 atoms
average map value = 0.07095, steps = 260
shifted from previous position = 2.45
rotated from previous position = 40.2 degrees
atoms outside contour = 1485, contour level = 0.027968
Position of 9hud (#38) relative to cryosparc_P483_J178_007_volume_map.mrc z
flip (#55) coordinates:
Matrix rotation and translation
0.68744757 0.35641921 0.63275685 15.52206548
0.28938953 0.66468217 -0.68880429 73.81019326
-0.66608526 0.65663002 0.35379014 216.09676949
Axis 0.71899263 0.69409402 -0.03582029
Axis point 0.00000000 -189.86123076 144.51310834
Rotation angle (degrees) 69.33153492
Shift along axis 54.65081588
> mmaker #8 to #38
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 9hud, chain A (#38) with 1ezx, chain A (#8), sequence alignment
score = 1674.4
RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
0.519)
> hide #!38 models
> select subtract #38
Nothing selected
> show #!8 models
> mmaker #7 to #8
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 1ezx, chain C (#8) with 5a0c, chain A (#7), sequence alignment
score = 241.2
RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
3.073)
> hide #!8 models
> show #7 models
> volume #55 level 0.03303
> open /Users/amy/Downloads/cryosparc_P483_J178_007_volume_map.mrc
Opened cryosparc_P483_J178_007_volume_map.mrc as #56, grid size 400,400,400,
pixel 0.723, shown at level 0.00984, step 2, values float32
> volume #56 level 0.0196
> close #56
> open /Users/amy/Downloads/cryosparc_P483_J179_005_volume_map.mrc
Opened cryosparc_P483_J179_005_volume_map.mrc as #56, grid size 400,400,400,
pixel 0.723, shown at level 0.00903, step 2, values float32
> open /Users/amy/Downloads/cryosparc_P483_J180_002_volume_map.mrc
Opened cryosparc_P483_J180_002_volume_map.mrc as #70, grid size 400,400,400,
pixel 0.723, shown at level 0.00199, step 2, values float32
> hide #!70 models
> show #!66 models
> hide #!66 models
> show #!67 models
> open /Users/amy/Downloads/cryosparc_P483_J183_007_volume_map.mrc
Opened cryosparc_P483_J183_007_volume_map.mrc as #71, grid size 400,400,400,
pixel 0.723, shown at level 0.0116, step 2, values float32
> hide #!67 models
> volume #71 level 0.03377
> volume #71 level 0.03909
> transparency #71 50
> hide #7 models
> show #!38 models
> select add #38
6282 atoms, 6138 bonds, 1077 residues, 1 model selected
> view matrix models
> #38,-0.91266,0.065596,-0.40341,292.72,0.36322,0.5827,-0.727,65.755,0.18738,-0.81003,-0.55564,148.75
> view matrix models
> #38,-0.72502,-0.2597,-0.63788,278.46,0.38017,0.62139,-0.68509,61.067,0.57429,-0.73921,-0.3518,82.291
> view matrix models
> #38,-0.72502,-0.2597,-0.63788,277.14,0.38017,0.62139,-0.68509,52.977,0.57429,-0.73921,-0.3518,86.091
> view matrix models
> #38,-0.65947,-0.28553,-0.69539,268.48,0.35515,0.69696,-0.62299,53.205,0.66254,-0.65781,-0.35822,69.098
> view matrix models
> #38,-0.65947,-0.28553,-0.69539,267.26,0.35515,0.69696,-0.62299,52.554,0.66254,-0.65781,-0.35822,69.625
> close #58-69
> fitmap #38 inMap #71
Fit molecule 9hud (#38) to map cryosparc_P483_J183_007_volume_map.mrc (#71)
using 6282 atoms
average map value = 0.07544, steps = 148
shifted from previous position = 7.45
rotated from previous position = 12.1 degrees
atoms outside contour = 1976, contour level = 0.039086
Position of 9hud (#38) relative to cryosparc_P483_J183_007_volume_map.mrc
(#71) coordinates:
Matrix rotation and translation
-0.67498701 -0.41761657 -0.60826719 272.94445864
0.34716985 0.54767448 -0.76126592 67.90283128
0.65104966 -0.72501662 -0.22468927 71.15250272
Axis 0.02459578 -0.85446836 0.51892087
Axis point 117.22275735 0.00000000 126.50966305
Rotation angle (degrees) 132.53192375
Shift along axis -14.38502000
> mmaker #8 to #38
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 9hud, chain A (#38) with 1ezx, chain A (#8), sequence alignment
score = 1674.4
RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
0.519)
> show #!8 models
> select subtract #38
Nothing selected
> hide #!38 models
> show #7 models
> mmaker #7 to #8
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 1ezx, chain C (#8) with 5a0c, chain A (#7), sequence alignment
score = 241.2
RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
3.073)
> hide #!8 models
> open "/Users/amy/Downloads/cryosparc_P371_J1247_003_volume_map (1).mrc"
Opened cryosparc_P371_J1247_003_volume_map (1).mrc as #58, grid size
300,300,300, pixel 0.867, shown at level 0.0217, step 2, values float32
> hide #7 models
> volume #58 level 0.07127
> transparency 58 50
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency #58 50
> select add #58
2 models selected
> select subtract #58
Nothing selected
> show #!57 models
> hide #!57 models
> show #!37 models
> select add #37
3984 atoms, 3982 bonds, 5 pseudobonds, 592 residues, 3 models selected
> view matrix models
> #37,-0.92665,0.37309,0.046068,189.97,-0.3746,-0.92671,-0.029877,215.08,0.031544,-0.044943,0.99849,41.461
> view matrix models
> #37,-0.95684,-0.22555,-0.18327,235.41,0.22555,-0.974,0.021102,173.18,-0.18327,-0.021145,0.98284,55.964
> view matrix models
> #37,-0.95684,-0.22555,-0.18327,230.3,0.22555,-0.974,0.021102,164.37,-0.18327,-0.021145,0.98284,103.6
> view matrix models
> #37,-0.71551,-0.36432,-0.59609,244.23,0.27076,-0.93118,0.24412,146.37,-0.644,0.013275,0.76491,146.06
> view matrix models
> #37,-0.38059,-0.21113,-0.90032,230.74,0.23197,-0.96426,0.12806,157.34,-0.89517,-0.16011,0.41597,192.06
> view matrix models
> #37,-0.38059,-0.21113,-0.90032,226.85,0.23197,-0.96426,0.12806,158.76,-0.89517,-0.16011,0.41597,189.5
> fitmap #37 inMap #58
Fit molecule 1ezx (#37) to map cryosparc_P371_J1247_003_volume_map (1).mrc
(#58) using 3984 atoms
average map value = 0.0799, steps = 112
shifted from previous position = 8.44
rotated from previous position = 14 degrees
atoms outside contour = 1944, contour level = 0.071265
Position of 1ezx (#37) relative to cryosparc_P371_J1247_003_volume_map (1).mrc
(#58) coordinates:
Matrix rotation and translation
-0.34799611 0.02716421 -0.93710235 206.67239671
0.14052585 -0.98677538 -0.08078885 177.04596820
-0.92690409 -0.15980131 0.33957672 198.01665488
Axis -0.57025546 -0.07360376 0.81816330
Axis point 168.54356692 102.18640974 0.00000000
Rotation angle (degrees) 176.02747367
Shift along axis 31.12264873
> open "/Users/amy/Downloads/cryosparc_P371_J1247_003_volume_map (1).mrc"
Opened cryosparc_P371_J1247_003_volume_map (1).mrc as #59, grid size
300,300,300, pixel 0.867, shown at level 0.0217, step 2, values float32
> volume #59 level 0.06978
> hide #!58 models
> mmaker #7 to #37
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 1ezx, chain C (#37) with 5a0c, chain A (#7), sequence alignment
score = 241.2
RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
3.073)
> show #7 models
> hide #!59 models
> show #!58 models
> hide #!58 models
> show #!59 models
> transparency #59 50
> ui mousemode right "map eraser"
> hide #7 models
> hide #!37 models
> select subtract #37
Nothing selected
> volume erase #59 center 116.15,104.56,160.67 radius 47.97
Opened cryosparc_P371_J1247_003_volume_map (1).mrc copy as #61, grid size
300,300,300, pixel 0.867, shown at step 1, values float32
> volume erase #61 center 122.57,113.18,101.86 radius 47.97
> ui mousemode right "translate selected models"
> show #18 models
> select #18/A:202
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> rainbow sel
> select add #18
1883 atoms, 1745 bonds, 394 residues, 1 model selected
> select subtract #18
Nothing selected
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> hide #18 models
> show #7 models
> show #18 models
> mmaker #18 to #7
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 5a0c, chain A (#7) with copy of 5a0c, chain A (#18), sequence
alignment score = 1112.7
RMSD between 218 pruned atom pairs is 0.000 angstroms; (across all 218 pairs:
0.000)
> color #18 #ed91dfff
> color #18 #ebc5edff
> fitmap #7 inMap #59
Fit molecule 5a0c (#7) to map cryosparc_P371_J1247_003_volume_map (1).mrc
(#59) using 1883 atoms
average map value = 0.0522, steps = 120
shifted from previous position = 3.71
rotated from previous position = 23.2 degrees
atoms outside contour = 1476, contour level = 0.06978
Position of 5a0c (#7) relative to cryosparc_P371_J1247_003_volume_map (1).mrc
(#59) coordinates:
Matrix rotation and translation
-0.93248311 0.31677416 0.17357817 149.49808518
-0.24611565 -0.20545531 -0.94721444 169.75896469
-0.26439050 -0.92598178 0.26954669 154.83015425
Axis 0.02975759 0.61381323 -0.78889024
Axis point 98.48308815 127.59008236 0.00000000
Rotation angle (degrees) 159.09861794
Shift along axis -13.49499578
> hide #18 models
> ui mousemode right "map eraser"
> volume erase #61 center 140.38,143.93,165.02 radius 9.1821
> volume erase #61 center 135.35,144.22,156.8 radius 9.1821
> volume erase #61 center 126.68,146.69,162.17 radius 9.1821
> ui mousemode right "translate selected models"
> fitmap #7 inMap #59
Fit molecule 5a0c (#7) to map cryosparc_P371_J1247_003_volume_map (1).mrc
(#59) using 1883 atoms
average map value = 0.0522, steps = 48
shifted from previous position = 0.00729
rotated from previous position = 0.02 degrees
atoms outside contour = 1476, contour level = 0.06978
Position of 5a0c (#7) relative to cryosparc_P371_J1247_003_volume_map (1).mrc
(#59) coordinates:
Matrix rotation and translation
-0.93245587 0.31693119 0.17343780 149.49596389
-0.24610156 -0.20574256 -0.94715575 169.75337215
-0.26449966 -0.92586426 0.26984311 154.82942667
Axis 0.02983605 0.61368746 -0.78898511
Axis point 98.49093754 127.56704910 0.00000000
Rotation angle (degrees) 159.09569307
Shift along axis -13.52222698
> mmaker #7 to #18
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 copy of 5a0c, chain A (#18) with 5a0c, chain A (#7), sequence
alignment score = 1112.7
RMSD between 218 pruned atom pairs is 0.000 angstroms; (across all 218 pairs:
0.000)
> fitmap #7 inMap #59
Fit molecule 5a0c (#7) to map cryosparc_P371_J1247_003_volume_map (1).mrc
(#59) using 1883 atoms
average map value = 0.0522, steps = 120
shifted from previous position = 3.71
rotated from previous position = 23.2 degrees
atoms outside contour = 1476, contour level = 0.06978
Position of 5a0c (#7) relative to cryosparc_P371_J1247_003_volume_map (1).mrc
(#59) coordinates:
Matrix rotation and translation
-0.93249206 0.31673033 0.17361005 149.49824725
-0.24614085 -0.20547558 -0.94720350 169.75915732
-0.26433545 -0.92599227 0.26956462 154.82905865
Axis 0.02972878 0.61380618 -0.78889681
Axis point 98.47960888 127.58948855 0.00000000
Rotation angle (degrees) 159.09952411
Shift along axis -13.50053159
> volume #61 level 0.07557
> open /Users/amy/Downloads/cryosparc_P483_J188_006_volume_map.mrc
Opened cryosparc_P483_J188_006_volume_map.mrc as #60, grid size 400,400,400,
pixel 0.723, shown at level 0.0122, step 2, values float32
> volume #60 level 0.04049
> hide #7 models
> close #39-56
> transparency #60 50
> show #!57 models
> select add #57
1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 3 models selected
> select subtract #57
Nothing selected
> hide #!57 models
> show #!38 models
> select add #38
6282 atoms, 6138 bonds, 1077 residues, 1 model selected
> view matrix models
> #38,0.70129,-0.71169,-0.041051,59.454,0.277,0.32511,-0.9042,89.328,0.65685,0.62274,0.42514,10.395
> view matrix models
> #38,0.68049,0.72218,0.12406,5.6594,-0.15756,0.30955,-0.93774,159.08,-0.71562,0.61858,0.32443,228.89
> view matrix models
> #38,0.7111,0.6991,0.074864,2.3195,-0.17274,0.27693,-0.94523,162.83,-0.68154,0.65922,0.31769,222.03
> volume flip #60 axis z
Opened cryosparc_P483_J188_006_volume_map.mrc z flip as #39, grid size
400,400,400, pixel 0.723, shown at step 1, values float32
> view matrix models
> #38,-0.79214,-0.23105,-0.56492,283.77,0.39756,0.50697,-0.76481,61.539,0.4631,-0.83042,-0.30973,105.99
> view matrix models
> #38,-0.72246,-0.55636,-0.41051,283.31,0.053262,0.54717,-0.83532,115.33,0.68936,-0.62535,-0.36568,63.032
> view matrix models
> #38,-0.72246,-0.55636,-0.41051,283.27,0.053262,0.54717,-0.83532,115.31,0.68936,-0.62535,-0.36568,63.21
> view matrix models
> #38,-0.75346,-0.22412,-0.61812,278.02,0.32917,0.68524,-0.64969,64.051,0.56917,-0.69298,-0.44252,85.775
> view matrix models
> #38,-0.75346,-0.22412,-0.61812,277.72,0.32917,0.68524,-0.64969,62.337,0.56917,-0.69298,-0.44252,89.988
> view matrix models
> #38,-0.75346,-0.22412,-0.61812,274.8,0.32917,0.68524,-0.64969,60.25,0.56917,-0.69298,-0.44252,90.357
> fitmap #38 inMap #39
Fit molecule 9hud (#38) to map cryosparc_P483_J188_006_volume_map.mrc z flip
(#39) using 6282 atoms
average map value = 0.07719, steps = 140
shifted from previous position = 5.69
rotated from previous position = 10.5 degrees
atoms outside contour = 1975, contour level = 0.040487
Position of 9hud (#38) relative to cryosparc_P483_J188_006_volume_map.mrc z
flip (#39) coordinates:
Matrix rotation and translation
-0.69481285 -0.38668893 -0.60638839 274.92375859
0.29518489 0.61552849 -0.73074671 73.34577149
0.65582093 -0.68672881 -0.31353236 73.10268242
Axis 0.03066826 -0.87940971 0.47507687
Axis point 118.71936211 0.00000000 122.64604224
Rotation angle (degrees) 134.13955008
Shift along axis -21.34015667
> mmaker #37 to #38
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 9hud, chain A (#38) with 1ezx, chain A (#37), sequence alignment
score = 1674.4
RMSD between 330 pruned atom pairs is 0.490 angstroms; (across all 331 pairs:
0.519)
> select subtract #38
Nothing selected
> show #!37 models
> hide #!38 models
> show #!57 models
> mmaker #57 to #37
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 1ezx, chain C (#37) with copy of 1ezx, chain C (#57), sequence
alignment score = 1096
RMSD between 140 pruned atom pairs is 0.000 angstroms; (across all 140 pairs:
0.000)
> hide #!37 models
> select add #57
1009 atoms, 1014 bonds, 5 pseudobonds, 155 residues, 3 models selected
> view matrix models
> #57,-0.96139,-0.27328,-0.032326,225.27,0.26293,-0.87755,-0.40098,194.89,0.081212,-0.39399,0.91552,76.751
> view matrix models
> #57,-0.98395,-0.080553,-0.1592,229.11,0.11527,-0.96807,-0.2226,199.83,-0.13619,-0.23738,0.96182,88.362
> view matrix models
> #57,-0.98395,-0.080553,-0.1592,229.13,0.11527,-0.96807,-0.2226,200.95,-0.13619,-0.23738,0.96182,87.592
> view matrix models
> #57,-0.94283,-0.24393,0.22707,209.83,0.18457,-0.94952,-0.25367,196.49,0.27748,-0.19726,0.94026,54.255
> view matrix models
> #57,-0.94283,-0.24393,0.22707,211.13,0.18457,-0.94952,-0.25367,198.21,0.27748,-0.19726,0.94026,55.521
> view matrix models
> #57,-0.93042,-0.31273,0.19109,213.56,0.19345,-0.86193,-0.46866,206.45,0.31127,-0.39909,0.86246,61.443
> view matrix models
> #57,-0.93042,-0.31273,0.19109,212.58,0.19345,-0.86193,-0.46866,206.1,0.31127,-0.39909,0.86246,60.836
> view matrix models
> #57,-0.84274,-0.44664,0.3005,202.99,0.29429,-0.84967,-0.43756,196.06,0.45076,-0.28032,0.84749,47.549
> view matrix models
> #57,-0.84274,-0.44664,0.3005,204.01,0.29429,-0.84967,-0.43756,196.43,0.45076,-0.28032,0.84749,48.186
> view matrix models
> #57,-0.84274,-0.44664,0.3005,205.89,0.29429,-0.84967,-0.43756,195.12,0.45076,-0.28032,0.84749,50.177
> view matrix models
> #57,-0.40829,-0.80923,0.42242,172.87,0.75449,-0.55964,-0.34285,146.27,0.51385,0.17873,0.83905,34.853
> view matrix models
> #57,-0.40829,-0.80923,0.42242,177.69,0.75449,-0.55964,-0.34285,148.99,0.51385,0.17873,0.83905,33.682
> view matrix models
> #57,-0.26229,-0.78164,0.56591,157.89,0.82741,-0.48394,-0.28493,138.37,0.49658,0.39351,0.77367,33.446
> view matrix models
> #57,-0.50448,-0.84508,0.17704,198.87,0.77252,-0.53335,-0.34461,147.01,0.38565,-0.037082,0.9219,44.834
> view matrix models
> #57,-0.50448,-0.84508,0.17704,197.7,0.77252,-0.53335,-0.34461,146.01,0.38565,-0.037082,0.9219,43.5
> view matrix models
> #57,-0.55352,-0.81516,0.17067,201.3,0.76006,-0.57821,-0.29661,145.6,0.34047,-0.03446,0.93962,46.193
> view matrix models
> #57,-0.55352,-0.81516,0.17067,201,0.76006,-0.57821,-0.29661,144.01,0.34047,-0.03446,0.93962,46.083
> view matrix models
> #57,0.19927,-0.70806,0.67745,111.26,0.40682,-0.56916,-0.71453,193.98,0.89151,0.41799,0.17463,30.057
> fitmap #57 inMap #39
Fit molecule copy of 1ezx (#57) to map cryosparc_P483_J188_006_volume_map.mrc
z flip (#39) using 1009 atoms
average map value = 0.0293, steps = 168
shifted from previous position = 3.46
rotated from previous position = 14.9 degrees
atoms outside contour = 704, contour level = 0.040487
Position of copy of 1ezx (#57) relative to
cryosparc_P483_J188_006_volume_map.mrc z flip (#39) coordinates:
Matrix rotation and translation
-0.00776067 -0.76663470 0.64203663 129.30975418
0.53267917 -0.54654599 -0.64617367 178.30805215
0.84628169 0.33698479 0.41261190 20.94708234
Axis 0.59871569 -0.12437946 0.79124539
Axis point -5.11418337 119.30863791 0.00000000
Rotation angle (degrees) 124.80933717
Shift along axis 71.81620095
> view matrix models
> #57,-0.84354,-0.47018,0.25957,209.7,0.35522,-0.85092,-0.38698,186.48,0.40282,-0.23422,0.8848,45.964
> view matrix models
> #57,-0.84354,-0.47018,0.25957,210.5,0.35522,-0.85092,-0.38698,187.68,0.40282,-0.23422,0.8848,46.627
> view matrix models
> #57,-0.91572,-0.40165,-0.011594,228.63,0.39352,-0.89061,-0.22795,177.36,0.081229,-0.2133,0.9736,67.651
> view matrix models
> #57,-0.91572,-0.40165,-0.011594,228.49,0.39352,-0.89061,-0.22795,177.31,0.081229,-0.2133,0.9736,67.495
> fitmap #57 inMap #39
Fit molecule copy of 1ezx (#57) to map cryosparc_P483_J188_006_volume_map.mrc
z flip (#39) using 1009 atoms
average map value = 0.03023, steps = 128
shifted from previous position = 2.17
rotated from previous position = 27.6 degrees
atoms outside contour = 692, contour level = 0.040487
Position of copy of 1ezx (#57) relative to
cryosparc_P483_J188_006_volume_map.mrc z flip (#39) coordinates:
Matrix rotation and translation
-0.97588300 -0.21795429 0.01217931 226.13416383
0.16332980 -0.76604383 -0.62169145 212.61271533
0.14483021 -0.60470887 0.78316756 80.91608083
Axis 0.04203015 -0.32829732 0.94363888
Axis point 99.48152797 132.57508735 0.00000000
Rotation angle (degrees) 168.34438880
Shift along axis 16.05982811
> select subtract #57
Nothing selected
> volume gaussian #39 sDev 2
Opened cryosparc_P483_J188_006_volume_map.mrc z flip gaussian as #40, grid
size 400,400,400, pixel 0.723, shown at step 1, values float32
> open /Users/amy/Downloads/cryosparc_P483_molmap_of_combined_6A.mrc
Opened cryosparc_P483_molmap_of_combined_6A.mrc as #41, grid size 200,200,200,
pixel 1, shown at level 0.293, step 1, values float32
> transparency #41 50
> show #!37 models
> select add #37
3984 atoms, 3982 bonds, 5 pseudobonds, 592 residues, 3 models selected
> view matrix models
> #37,-0.96139,-0.27328,-0.032326,218.59,0.26293,-0.87755,-0.40098,146.69,0.081212,-0.39399,0.91552,81.851
> view matrix models
> #37,-0.049922,0.49391,-0.86808,164.61,0.32699,-0.81318,-0.48148,143.6,-0.94371,-0.30789,-0.12091,207.3
> view matrix models
> #37,0.78493,0.53816,-0.30703,72.795,0.33958,-0.78815,-0.51332,143.29,-0.51824,0.29866,-0.80139,186.1
> view matrix models
> #37,0.48345,-0.22115,0.84698,66.159,0.004741,-0.96689,-0.25517,160.69,0.87536,0.12738,-0.46639,79.548
> view matrix models
> #37,-0.49427,-0.19074,0.84812,131.98,0.13352,-0.98071,-0.14275,146.1,0.85899,0.04269,0.51021,29.25
> view matrix models
> #37,-0.87073,-0.2065,0.44631,181.66,0.14198,-0.97448,-0.17389,146.97,0.47082,-0.088043,0.87782,41.66
> view matrix models
> #37,-0.87073,-0.2065,0.44631,183.6,0.14198,-0.97448,-0.17389,140.36,0.47082,-0.088043,0.87782,41.006
> view matrix models
> #37,-0.83015,0.067283,-0.55346,223.99,0.083286,-0.96659,-0.24243,147.91,-0.55128,-0.24735,0.79681,124.17
> view matrix models
> #37,-0.83015,0.067283,-0.55346,229.16,0.083286,-0.96659,-0.24243,155.6,-0.55128,-0.24735,0.79681,121.21
> view matrix models
> #37,-0.76415,-0.19095,-0.61612,241.25,0.333,-0.93483,-0.12329,129.98,-0.55243,-0.29938,0.77794,124.99
> fitmap #37 inMap #41
Fit molecule 1ezx (#37) to map cryosparc_P483_molmap_of_combined_6A.mrc (#41)
using 3984 atoms
average map value = 0.4227, steps = 272
shifted from previous position = 34.2
rotated from previous position = 34.8 degrees
atoms outside contour = 366, contour level = 0.29336
Position of 1ezx (#37) relative to cryosparc_P483_molmap_of_combined_6A.mrc
(#41) coordinates:
Matrix rotation and translation
-0.39076986 0.10890222 -0.91402362 198.79794072
0.07022585 -0.98655567 -0.14756757 150.28581374
-0.91780564 -0.12185304 0.37786848 136.15090391
Axis 0.55183393 0.08116225 -0.82999519
Axis point 145.70964793 80.43889324 0.00000000
Rotation angle (degrees) 178.66493597
Shift along axis 8.89638759
> mmaker #7 to #37
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 1ezx, chain C (#37) with 5a0c, chain A (#7), sequence alignment
score = 241.2
RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
3.073)
> show #7 models
> show #!8 models
> mmaker #8 to #7
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 5a0c, chain A (#7) with 1ezx, chain C (#8), sequence alignment
score = 241.2
RMSD between 91 pruned atom pairs is 1.047 angstroms; (across all 129 pairs:
3.073)
> select #8/A
2686 atoms, 2674 bonds, 398 residues, 1 model selected
> delete #8/A
> select #8/B
289 atoms, 294 bonds, 39 residues, 1 model selected
> delete #8/B
> close #8
> show #!31 models
> mmaker #31 t o#7
> matchmaker #31 to o#7
Invalid "to" argument: invalid atoms specifier
> mmaker #31 t to#7
> matchmaker #31 to to#7
Invalid "to" argument: invalid atoms specifier
> mmaker #31 to #7
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 5a0c, chain A (#7) with copy of copy of copy of 1ezx, chain A
(#31), sequence alignment score = 25.4
RMSD between 4 pruned atom pairs is 1.006 angstroms; (across all 34 pairs:
19.211)
> mmaker #31 to #37
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 1ezx, chain A (#37) with copy of copy of copy of 1ezx, chain A
(#31), sequence alignment score = 1734
RMSD between 335 pruned atom pairs is 0.000 angstroms; (across all 335 pairs:
0.000)
> hide #!37 models
> hide #!41 models
> hide #!57 models
> combine #7,31 modelId #42 name AATHNEcombined
Remapping chain ID 'A' in copy of copy of copy of 1ezx #31 to 'C'
> hide #!31 models
> hide #7 models
> molmap #42 6
Opened AATHNEcombined map 6 as #8, grid size 43,51,63, pixel 2, shown at level
0.107, step 1, values float32
> volume #8 level 0.4678
> hide #!42 models
> volume #8 level 0.4143
> transparency #8 50
> show #!29 models
> select add #8
2 models selected
> view matrix models
> #8,-0.94731,0.3033,-0.10305,152.68,-0.052376,-0.46403,-0.88427,177.46,-0.31602,-0.83228,0.45547,210.1
> view matrix models
> #8,-0.67966,0.68715,-0.25667,146.07,0.0014291,-0.34867,-0.93725,176.15,-0.73352,-0.63738,0.23599,220.93
> select subtract #8
Nothing selected
> select add #8
2 models selected
> view matrix models
> #8,-0.80209,0.59535,-0.046957,144.36,-0.15685,-0.28587,-0.94534,180.87,-0.57624,-0.75089,0.32268,217.17
> view matrix models
> #8,-0.98552,0.057058,-0.15966,159.48,0.11645,-0.45668,-0.88198,176.33,-0.12324,-0.8878,0.44342,206.47
> select subtract #8
Nothing selected
> fitmap #8 inMap #29
Fit map AATHNEcombined map 6 in map J1122.mrc using 3370 points
correlation = -0.06744, correlation about mean = 0.03351, overlap = -0.3948
steps = 72, shift = 3.07, angle = 5.37 degrees
Position of AATHNEcombined map 6 (#8) relative to J1122.mrc (#29) coordinates:
Matrix rotation and translation
-0.99402372 -0.01790342 -0.10768616 160.40909895
0.10457674 -0.43913839 -0.89231227 175.73306960
-0.03131369 -0.89824103 0.43838626 207.83747749
Axis -0.04104025 -0.52866794 0.84783601
Axis point 80.62201678 156.15315639 0.00000000
Rotation angle (degrees) 175.85785915
Shift along axis 76.72442836
> volume #8 level 0.3659
> view
> volume #29 level 0.06441
> show #!42 models
> select add #42
4858 atoms, 4713 bonds, 831 residues, 1 model selected
> view matrix models
> #42,-0.94731,0.3033,-0.10305,202.51,-0.052376,-0.46403,-0.88427,151.25,-0.31602,-0.83228,0.45547,188.42
> view matrix models
> #42,-0.065313,0.66691,-0.74227,198.13,-0.22175,-0.73496,-0.64083,151.68,-0.97291,0.12274,0.19589,194.19
> view matrix models
> #42,0.76996,0.12763,-0.6252,186.82,-0.51684,-0.44988,-0.72835,155.58,-0.37422,0.88392,-0.28042,184.85
> view matrix models
> #42,0.26956,0.68406,-0.67779,189.68,-0.23721,-0.63498,-0.73521,153.14,-0.93331,0.35896,-0.0088999,195.67
> view matrix models
> #42,0.16808,0.4812,-0.86035,199.68,0.12383,-0.87616,-0.46585,142.27,-0.97797,-0.028238,-0.20685,207.72
> view matrix models
> #42,0.16808,0.4812,-0.86035,176.9,0.12383,-0.87616,-0.46585,168.91,-0.97797,-0.028238,-0.20685,243.77
> view matrix models
> #42,-0.098371,0.74921,-0.65499,172.34,0.16185,-0.63737,-0.75337,172.69,-0.9819,-0.18012,-0.058563,241.94
> view matrix models
> #42,-0.098371,0.74921,-0.65499,168.3,0.16185,-0.63737,-0.75337,164.55,-0.9819,-0.18012,-0.058563,240.14
> fitmap #42 inMap #8
Fit molecule AATHNEcombined (#42) to map AATHNEcombined map 6 (#8) using 4858
atoms
average map value = 0.4401, steps = 236
shifted from previous position = 23.5
rotated from previous position = 81.6 degrees
atoms outside contour = 1171, contour level = 0.36586
Position of AATHNEcombined (#42) relative to AATHNEcombined map 6 (#8)
coordinates:
Matrix rotation and translation
0.99999997 0.00012320 0.00021381 -0.02142066
-0.00012322 0.99999999 0.00009509 0.00213481
-0.00021379 -0.00009512 0.99999997 0.00632785
Axis -0.35962131 0.80845713 -0.46590727
Axis point 43.71009619 0.00000000 89.29249519
Rotation angle (degrees) 0.01515213
Shift along axis 0.00648103
> select subtract #42
Nothing selected
> hide #!42 models
> show #!42 models
> combine #42 close false
> select add #43
4858 atoms, 4713 bonds, 831 residues, 1 model selected
> view matrix models
> #43,-0.994,-0.018016,-0.1079,166.09,0.10482,-0.43904,-0.89233,181.76,-0.031297,-0.89829,0.43829,253.22
> view matrix models
> #43,-0.994,-0.018016,-0.1079,167.72,0.10482,-0.43904,-0.89233,183.32,-0.031297,-0.89829,0.43829,266.56
> select subtract #43
Nothing selected
> hide #!42 models
> select add #43/A:94
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #43/A:93
20 atoms, 19 bonds, 2 residues, 1 model selected
> select add #43/A:92
28 atoms, 26 bonds, 3 residues, 1 model selected
> select add #43/A:91
39 atoms, 36 bonds, 4 residues, 1 model selected
> select add #43/A:90
48 atoms, 44 bonds, 5 residues, 1 model selected
> select add #43/A:89
55 atoms, 50 bonds, 6 residues, 1 model selected
> select add #43/A:88
60 atoms, 54 bonds, 7 residues, 1 model selected
> select add #43/A:87
71 atoms, 65 bonds, 8 residues, 1 model selected
> select add #43/A:86
78 atoms, 71 bonds, 9 residues, 1 model selected
> select subtract #43/A:86
71 atoms, 65 bonds, 8 residues, 1 model selected
> select add #43/A:86
78 atoms, 71 bonds, 9 residues, 1 model selected
> select add #43/A:85
87 atoms, 79 bonds, 10 residues, 1 model selected
> select add #43/A:84
98 atoms, 89 bonds, 11 residues, 1 model selected
> select add #43/A:83
105 atoms, 95 bonds, 12 residues, 1 model selected
> select add #43/A:82
112 atoms, 102 bonds, 13 residues, 1 model selected
> select add #43/A:81
121 atoms, 110 bonds, 14 residues, 1 model selected
> select add #43/A:80
132 atoms, 120 bonds, 15 residues, 1 model selected
> select add #43/A:79
143 atoms, 130 bonds, 16 residues, 1 model selected
> select add #43/A:77
151 atoms, 137 bonds, 17 residues, 1 model selected
> select add #43/A:78
157 atoms, 142 bonds, 18 residues, 1 model selected
> select add #43/A:76
165 atoms, 149 bonds, 19 residues, 1 model selected
> select add #43/A:75
175 atoms, 159 bonds, 20 residues, 1 model selected
> select add #43/A:74
180 atoms, 163 bonds, 21 residues, 1 model selected
> select add #43/A:73
184 atoms, 166 bonds, 22 residues, 1 model selected
> select add #43/A:72
192 atoms, 173 bonds, 23 residues, 1 model selected
> select add #43/A:71
199 atoms, 179 bonds, 24 residues, 1 model selected
> select add #43/A:70
206 atoms, 185 bonds, 25 residues, 1 model selected
> select add #43/A:69
217 atoms, 195 bonds, 26 residues, 1 model selected
> select add #43/A:54
223 atoms, 200 bonds, 27 residues, 1 model selected
> select subtract #43/A:54
217 atoms, 195 bonds, 26 residues, 1 model selected
> select add #43/A:68
224 atoms, 201 bonds, 27 residues, 1 model selected
> select add #43/A:66
229 atoms, 205 bonds, 28 residues, 1 model selected
> select add #43/A:65
240 atoms, 215 bonds, 29 residues, 1 model selected
> select add #43/A:64
247 atoms, 221 bonds, 30 residues, 1 model selected
> select add #43/A:63
255 atoms, 228 bonds, 31 residues, 1 model selected
> select add #43/A:62
262 atoms, 234 bonds, 32 residues, 1 model selected
> select add #43/A:61
270 atoms, 241 bonds, 33 residues, 1 model selected
> select add #43/A:60
275 atoms, 245 bonds, 34 residues, 1 model selected
> select add #43/A:59
282 atoms, 251 bonds, 35 residues, 1 model selected
> select add #43/A:58
288 atoms, 256 bonds, 36 residues, 1 model selected
> select add #43/A:57
298 atoms, 266 bonds, 37 residues, 1 model selected
> select add #43/A:56
303 atoms, 270 bonds, 38 residues, 1 model selected
> select add #43/A:55
308 atoms, 274 bonds, 39 residues, 1 model selected
> select add #43/A:54
314 atoms, 279 bonds, 40 residues, 1 model selected
> select add #43/A:53
322 atoms, 286 bonds, 41 residues, 1 model selected
> select add #43/A:52
329 atoms, 292 bonds, 42 residues, 1 model selected
> select add #43/A:51
340 atoms, 303 bonds, 43 residues, 1 model selected
> select add #43/A:50
348 atoms, 310 bonds, 44 residues, 1 model selected
> select add #43/A:48
353 atoms, 314 bonds, 45 residues, 1 model selected
> select add #43/A:47
361 atoms, 321 bonds, 46 residues, 1 model selected
> select add #43/A:46
369 atoms, 328 bonds, 47 residues, 1 model selected
> select subtract #43/A:46
361 atoms, 321 bonds, 46 residues, 1 model selected
> select add #43/A:45
368 atoms, 327 bonds, 47 residues, 1 model selected
> select add #43/A:46
376 atoms, 334 bonds, 48 residues, 1 model selected
> select add #43/A:44
381 atoms, 338 bonds, 49 residues, 1 model selected
> select add #43/A:43
385 atoms, 341 bonds, 50 residues, 1 model selected
> select add #43/A:42
391 atoms, 346 bonds, 51 residues, 1 model selected
> select add #43/A:41
402 atoms, 357 bonds, 52 residues, 1 model selected
> select add #43/A:40
412 atoms, 367 bonds, 53 residues, 1 model selected
> select add #43/A:39
416 atoms, 370 bonds, 54 residues, 1 model selected
> color sel forest green
> select clear
> select add #43/A:49
7 atoms, 7 bonds, 1 residue, 1 model selected
> color sel forest green
> select clear
> select add #43/A:38
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #43/A:36
15 atoms, 13 bonds, 2 residues, 1 model selected
> select add #43/A:35
23 atoms, 20 bonds, 3 residues, 1 model selected
> select add #43/A:34
32 atoms, 28 bonds, 4 residues, 1 model selected
> select add #43/A:33
40 atoms, 35 bonds, 5 residues, 1 model selected
> select add #43/A:32
46 atoms, 40 bonds, 6 residues, 1 model selected
> select subtract #43/A:32
40 atoms, 35 bonds, 5 residues, 1 model selected
> select add #43/A:32
46 atoms, 40 bonds, 6 residues, 1 model selected
> select add #43/A:31
53 atoms, 46 bonds, 7 residues, 1 model selected
> select add #43/A:30
61 atoms, 53 bonds, 8 residues, 1 model selected
> color sel forest green
> select clear
> select add #43/A:108
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #43/A:109
15 atoms, 13 bonds, 2 residues, 1 model selected
> select add #43/A:110
23 atoms, 20 bonds, 3 residues, 1 model selected
> select add #43/A:111
32 atoms, 28 bonds, 4 residues, 1 model selected
> select add #43/A:112
40 atoms, 35 bonds, 5 residues, 1 model selected
> color sel cyan
> select add #43/A:90
49 atoms, 43 bonds, 6 residues, 1 model selected
> select add #43/A:91
60 atoms, 53 bonds, 7 residues, 1 model selected
> select add #43/A:92
68 atoms, 60 bonds, 8 residues, 1 model selected
> select add #43/A:93
79 atoms, 71 bonds, 9 residues, 1 model selected
> select add #43/A:94
88 atoms, 79 bonds, 10 residues, 1 model selected
> color sel cyan
> select add #43/A:54
94 atoms, 84 bonds, 11 residues, 1 model selected
> select add #43/A:53
102 atoms, 91 bonds, 12 residues, 1 model selected
> select add #43/A:52
109 atoms, 97 bonds, 13 residues, 1 model selected
> select add #43/A:51
120 atoms, 108 bonds, 14 residues, 1 model selected
> color sel cyan
> select clear
> show #!42 models
> hide #!42 models
> show #!42 models
> hide #!42 models
> hide #!43 models
> show #!43 models
> combine #43 close false
> select add #44
4858 atoms, 4713 bonds, 831 residues, 1 model selected
> view matrix models
> #44,-0.994,-0.018016,-0.1079,181.57,0.10482,-0.43904,-0.89233,189.57,-0.031297,-0.89829,0.43829,312.85
> select subtract #44
Nothing selected
> select add #44/A:127
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #44/A:128
15 atoms, 14 bonds, 2 residues, 1 model selected
> delete sel
> select add #44/A:129
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #44/A:130
14 atoms, 12 bonds, 2 residues, 1 model selected
> select add #44/A:131
18 atoms, 15 bonds, 3 residues, 1 model selected
> select add #44/A:132
29 atoms, 25 bonds, 4 residues, 1 model selected
> select add #44/A:133
40 atoms, 35 bonds, 5 residues, 1 model selected
> select add #44/A:134
48 atoms, 42 bonds, 6 residues, 1 model selected
> select subtract #44/A:134
40 atoms, 35 bonds, 5 residues, 1 model selected
> select add #44/A:134
48 atoms, 42 bonds, 6 residues, 1 model selected
> select add #44/A:135
52 atoms, 45 bonds, 7 residues, 1 model selected
> select add #44/A:136
60 atoms, 52 bonds, 8 residues, 1 model selected
> select add #44/A:137
64 atoms, 55 bonds, 9 residues, 1 model selected
> select add #44/A:138
71 atoms, 61 bonds, 10 residues, 1 model selected
> delete sel
> select add #44/A:96
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #44/A:97
12 atoms, 10 bonds, 2 residues, 1 model selected
> select add #44/A:98
24 atoms, 22 bonds, 3 residues, 1 model selected
> select add #44/A:99
32 atoms, 29 bonds, 4 residues, 1 model selected
> select add #44/A:100
39 atoms, 36 bonds, 5 residues, 1 model selected
> select add #44/A:101
46 atoms, 42 bonds, 6 residues, 1 model selected
> select add #44/A:102
54 atoms, 49 bonds, 7 residues, 1 model selected
> select add #44/A:103
62 atoms, 56 bonds, 8 residues, 1 model selected
> select add #44/A:104
70 atoms, 63 bonds, 9 residues, 1 model selected
> select add #44/A:105
78 atoms, 70 bonds, 10 residues, 1 model selected
> select add #44/A:106
86 atoms, 77 bonds, 11 residues, 1 model selected
> select add #44/A:107
94 atoms, 84 bonds, 12 residues, 1 model selected
> delete sel
> select clear
> select add #44/A:160
9 atoms, 8 bonds, 1 residue, 1 model selected
> select subtract #44/A:160
Nothing selected
> select #44/A:159
8 atoms, 7 bonds, 1 residue, 1 model selected
> select subtract #44/A:159
Nothing selected
> select add #44/A:159
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #44/A:158
15 atoms, 13 bonds, 2 residues, 1 model selected
> select add #44/A:157
21 atoms, 18 bonds, 3 residues, 1 model selected
> select add #44/A:156
26 atoms, 22 bonds, 4 residues, 1 model selected
> select add #44/A:155
34 atoms, 29 bonds, 5 residues, 1 model selected
> select add #44/A:154
38 atoms, 32 bonds, 6 residues, 1 model selected
> select add #44/A:152
49 atoms, 42 bonds, 7 residues, 1 model selected
> select add #44/A:151
57 atoms, 49 bonds, 8 residues, 1 model selected
> select add #44/A:150
68 atoms, 59 bonds, 9 residues, 1 model selected
> select add #44/A:149
72 atoms, 62 bonds, 10 residues, 1 model selected
> select add #44/A:148
80 atoms, 69 bonds, 11 residues, 1 model selected
> select add #44/A:147
88 atoms, 76 bonds, 12 residues, 1 model selected
> select add #44/A:146
92 atoms, 79 bonds, 13 residues, 1 model selected
> select add #44/A:145
106 atoms, 94 bonds, 14 residues, 1 model selected
> delete sel
> select add #44/A:113
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #44/A:114
12 atoms, 10 bonds, 2 residues, 1 model selected
> select add #44/A:115
18 atoms, 15 bonds, 3 residues, 1 model selected
> select add #44/A:116
23 atoms, 19 bonds, 4 residues, 1 model selected
> select add #44/A:117
30 atoms, 25 bonds, 5 residues, 1 model selected
> select add #44/A:118
38 atoms, 32 bonds, 6 residues, 1 model selected
> select add #44/A:119
46 atoms, 39 bonds, 7 residues, 1 model selected
> select add #44/A:120
51 atoms, 43 bonds, 8 residues, 1 model selected
> select add #44/A:121
59 atoms, 50 bonds, 9 residues, 1 model selected
> select add #44/A:122
66 atoms, 56 bonds, 10 residues, 1 model selected
> select add #44/A:124
73 atoms, 62 bonds, 11 residues, 1 model selected
> select add #44/A:125
78 atoms, 66 bonds, 12 residues, 1 model selected
> select add #44/A:126
87 atoms, 74 bonds, 13 residues, 1 model selected
> delete sel
> open /Users/amy/Downloads/emd_8220.map
Opened emd_8220.map as #45, grid size 100,86,100, pixel 0.554,0.564,0.577,
shown at level 0.0696, step 1, values float32
> volume #45 level 0.05639
> close #45
> select add #44/A:16
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #44/A:17
15 atoms, 13 bonds, 2 residues, 1 model selected
> select add #44/A:18
19 atoms, 16 bonds, 3 residues, 1 model selected
> select add #44/A:19
23 atoms, 19 bonds, 4 residues, 1 model selected
> select add #44/A:20
34 atoms, 29 bonds, 5 residues, 1 model selected
> select add #44/A:21
45 atoms, 39 bonds, 6 residues, 1 model selected
> select add #44/A:22
50 atoms, 43 bonds, 7 residues, 1 model selected
> select add #44/A:23
61 atoms, 53 bonds, 8 residues, 1 model selected
> select add #44/A:24
68 atoms, 60 bonds, 9 residues, 1 model selected
> select add #44/A:25
78 atoms, 70 bonds, 10 residues, 1 model selected
> select add #44/A:26
83 atoms, 74 bonds, 11 residues, 1 model selected
> select add #44/A:27
97 atoms, 89 bonds, 12 residues, 1 model selected
> select add #44/A:29
108 atoms, 100 bonds, 13 residues, 1 model selected
> delete sel
> select add #44
4377 atoms, 4217 bonds, 5 pseudobonds, 767 residues, 2 models selected
> view matrix models
> #44,-0.994,-0.018016,-0.1079,167.02,0.10482,-0.43904,-0.89233,176.04,-0.031297,-0.89829,0.43829,207.55
> fitmap #44 inMap #8
Fit molecule copy of copy of AATHNEcombined (#44) to map AATHNEcombined map 6
(#8) using 4377 atoms
average map value = 0.4393, steps = 56
shifted from previous position = 6.58
rotated from previous position = 0.0611 degrees
atoms outside contour = 1072, contour level = 0.36586
Position of copy of copy of AATHNEcombined (#44) relative to AATHNEcombined
map 6 (#8) coordinates:
Matrix rotation and translation
0.99999971 0.00068256 0.00033276 -0.05114740
-0.00068229 0.99999944 -0.00080618 0.06249724
-0.00033331 0.00080595 0.99999962 -0.02902612
Axis 0.72788203 0.30072989 -0.61623801
Axis point 0.00000000 36.47000800 77.70180160
Rotation angle (degrees) 0.06345003
Shift along axis -0.00054749
> view matrix models
> #44,-0.99398,-0.018669,-0.108,161.2,0.10517,-0.43979,-0.89192,171.06,-0.030847,-0.89791,0.4391,163.49
> view matrix models
> #44,-0.99398,-0.018669,-0.108,160.92,0.10517,-0.43979,-0.89192,163.66,-0.030847,-0.89791,0.4391,148.99
> fitmap #44 inMap #29
Fit molecule copy of copy of AATHNEcombined (#44) to map J1122.mrc (#29) using
4377 atoms
average map value = 0.08017, steps = 120
shifted from previous position = 10.4
rotated from previous position = 19 degrees
atoms outside contour = 1934, contour level = 0.064406
Position of copy of copy of AATHNEcombined (#44) relative to J1122.mrc (#29)
coordinates:
Matrix rotation and translation
-0.93560766 0.29367131 -0.19594762 148.33622912
0.04403975 -0.45360760 -0.89011271 165.90577632
-0.35028390 -0.84142576 0.41146553 152.50362608
Axis 0.16365385 0.51877807 -0.83909876
Axis point 96.84111132 123.35674227 0.00000000
Rotation angle (degrees) 171.44551676
Shift along axis -17.62152966
> view matrix models
> #44,-0.93561,0.29367,-0.19595,147.21,0.04404,-0.45361,-0.89011,177.11,-0.35028,-0.84143,0.41147,212.36
> view matrix models
> #44,-0.93561,0.29367,-0.19595,156.61,0.04404,-0.45361,-0.89011,178.01,-0.35028,-0.84143,0.41147,216.59
> fitmap #44 inMap #8
Fit molecule copy of copy of AATHNEcombined (#44) to map AATHNEcombined map 6
(#8) using 4377 atoms
average map value = 0.4394, steps = 64
shifted from previous position = 3.67
rotated from previous position = 19 degrees
atoms outside contour = 1073, contour level = 0.36586
Position of copy of copy of AATHNEcombined (#44) relative to AATHNEcombined
map 6 (#8) coordinates:
Matrix rotation and translation
0.99999986 0.00044110 -0.00029615 0.00647815
-0.00044140 0.99999940 -0.00099710 0.04994382
0.00029571 0.00099723 0.99999946 -0.05779749
Axis 0.88254618 -0.26191484 -0.39052893
Axis point 0.00000000 52.03151904 54.05257298
Rotation angle (degrees) 0.06473724
Shift along axis 0.01520783
> view matrix models
> #44,-0.99405,-0.018449,-0.10737,168.43,0.10451,-0.43998,-0.8919,162.5,-0.030788,-0.89782,0.43929,154.17
> view matrix models
> #44,-0.99405,-0.018449,-0.10737,153.97,0.10451,-0.43998,-0.8919,165.28,-0.030788,-0.89782,0.43929,147.12
> fitmap #44 inMap #29
Fit molecule copy of copy of AATHNEcombined (#44) to map J1122.mrc (#29) using
4377 atoms
average map value = 0.08017, steps = 112
shifted from previous position = 3.23
rotated from previous position = 19 degrees
atoms outside contour = 1936, contour level = 0.064406
Position of copy of copy of AATHNEcombined (#44) relative to J1122.mrc (#29)
coordinates:
Matrix rotation and translation
-0.93553950 0.29370365 -0.19622436 148.34392039
0.04417583 -0.45387692 -0.88996867 165.89259865
-0.35044876 -0.84126922 0.41164519 152.49532201
Axis 0.16377458 0.51865136 -0.83915354
Axis point 96.84939042 123.33620103 0.00000000
Rotation angle (degrees) 171.44966078
Shift along axis -17.63160462
> select add #8
4377 atoms, 4217 bonds, 5 pseudobonds, 767 residues, 4 models selected
> select subtract #44
2 models selected
> view matrix models
> #8,-0.94817,0.24716,-0.1997,158.38,0.060761,-0.47584,-0.87743,176.64,-0.31189,-0.84409,0.43616,212.3
> select subtract #8
Nothing selected
> select add #44
4377 atoms, 4217 bonds, 5 pseudobonds, 767 residues, 2 models selected
> view matrix models
> #44,-0.93554,0.2937,-0.19622,141.41,0.044176,-0.45388,-0.88997,179.93,-0.35045,-0.84127,0.41165,213.18
> view matrix models
> #44,-0.93554,0.2937,-0.19622,151.53,0.044176,-0.45388,-0.88997,179.57,-0.35045,-0.84127,0.41165,212.38
> view matrix models
> #44,-0.93554,0.2937,-0.19622,155.41,0.044176,-0.45388,-0.88997,178.43,-0.35045,-0.84127,0.41165,216.37
> view matrix models
> #44,-0.93554,0.2937,-0.19622,155.54,0.044176,-0.45388,-0.88997,176.75,-0.35045,-0.84127,0.41165,213.56
> view matrix models
> #44,-0.93554,0.2937,-0.19622,156.39,0.044176,-0.45388,-0.88997,176.3,-0.35045,-0.84127,0.41165,214.67
> fitmap #44 inMap #8
Fit molecule copy of copy of AATHNEcombined (#44) to map AATHNEcombined map 6
(#8) using 4377 atoms
average map value = 0.4394, steps = 52
shifted from previous position = 1.68
rotated from previous position = 3.02 degrees
atoms outside contour = 1076, contour level = 0.36586
Position of copy of copy of AATHNEcombined (#44) relative to AATHNEcombined
map 6 (#8) coordinates:
Matrix rotation and translation
0.99999955 0.00082150 0.00046001 -0.00883030
-0.00082119 0.99999944 -0.00066348 0.04456765
-0.00046055 0.00066310 0.99999967 -0.03206776
Axis 0.57592008 0.39965178 -0.71315813
Axis point 36.92441346 35.72354775 0.00000000
Rotation angle (degrees) 0.06598750
Shift along axis 0.03559538
> select subtract #44
Nothing selected
> hide #!44 models
> select add #43
4858 atoms, 4713 bonds, 831 residues, 1 model selected
> select subtract #43
Nothing selected
> show #!44 models
> select add #44
4377 atoms, 4217 bonds, 5 pseudobonds, 767 residues, 2 models selected
> view matrix models
> #44,-0.94828,0.24625,-0.2003,158.56,0.061556,-0.47637,-0.87709,164.14,-0.3114,-0.84406,0.43658,152.21
> view matrix models
> #44,-0.94828,0.24625,-0.2003,153.59,0.061556,-0.47637,-0.87709,162.81,-0.3114,-0.84406,0.43658,148.12
> fitmap #44 inMap #29
Fit molecule copy of copy of AATHNEcombined (#44) to map J1122.mrc (#29) using
4377 atoms
average map value = 0.08017, steps = 96
shifted from previous position = 5.9
rotated from previous position = 3.02 degrees
atoms outside contour = 1937, contour level = 0.064406
Position of copy of copy of AATHNEcombined (#44) relative to J1122.mrc (#29)
coordinates:
Matrix rotation and translation
-0.93556337 0.29370123 -0.19611414 148.34082953
0.04407128 -0.45387887 -0.88997286 165.89641444
-0.35039819 -0.84126901 0.41168865 152.49037322
Axis 0.16372475 0.51864729 -0.83916578
Axis point 96.84588182 123.33307757 0.00000000
Rotation angle (degrees) 171.44626082
Shift along axis -17.63591277
> view matrix models
> #44,-0.93556,0.2937,-0.19611,181.55,0.044071,-0.45388,-0.88997,200.58,-0.3504,-0.84127,0.41169,325.24
> volume #29 level 0.05579
> volume #29 level 0.0639
> select subtract #44
Nothing selected
> select add #44/A:83
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #44/A:81
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #44/A:82
23 atoms, 21 bonds, 3 residues, 1 model selected
> select add #44/A:80
34 atoms, 31 bonds, 4 residues, 1 model selected
> select add #44/A:79
45 atoms, 41 bonds, 5 residues, 1 model selected
> select add #44/A:78
51 atoms, 46 bonds, 6 residues, 1 model selected
> select add #44/A:77
59 atoms, 53 bonds, 7 residues, 1 model selected
> select add #44/A:76
67 atoms, 60 bonds, 8 residues, 1 model selected
> select add #44/A:75
77 atoms, 70 bonds, 9 residues, 1 model selected
> delete sel
> select add #44/A:231
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #44/A:230
10 atoms, 8 bonds, 2 residues, 1 model selected
> select add #44/A:228
15 atoms, 12 bonds, 3 residues, 1 model selected
> select add #44/A:227
21 atoms, 17 bonds, 4 residues, 1 model selected
> select add #44/A:226
25 atoms, 20 bonds, 5 residues, 1 model selected
> select add #44/A:232
33 atoms, 27 bonds, 6 residues, 1 model selected
> select add #44/A:143
41 atoms, 34 bonds, 7 residues, 1 model selected
> select subtract #44/A:143
33 atoms, 27 bonds, 6 residues, 1 model selected
> select add #44/A:233
45 atoms, 39 bonds, 7 residues, 1 model selected
> delete sel
> select add #44/A:190
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #44/A:191
15 atoms, 13 bonds, 2 residues, 1 model selected
> select add #44/A:192
26 atoms, 23 bonds, 3 residues, 1 model selected
> select add #44/A:194
35 atoms, 31 bonds, 4 residues, 1 model selected
> select add #44/A:195
40 atoms, 35 bonds, 5 residues, 1 model selected
> select add #44/A:196
44 atoms, 38 bonds, 6 residues, 1 model selected
> delete sel
> select add #44/A:197
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #44/A:198
13 atoms, 11 bonds, 2 residues, 1 model selected
> delete sel
> hide #!44 models
> show #!44 models
> molmap #44 6
Opened copy of copy of AATHNEcombined map 6 as #45, grid size 43,51,63, pixel
2, shown at level 0.0888, step 1, values float32
> close #45
> molmap #44 4
Opened copy of copy of AATHNEcombined map 4 as #45, grid size 55,68,86, pixel
1.33, shown at level 0.0965, step 1, values float32
> hide #!45 models
> close #45
> molmap #44 6
Opened copy of copy of AATHNEcombined map 6 as #45, grid size 43,51,63, pixel
2, shown at level 0.0888, step 1, values float32
> volume #29 level 0.07099
> volume #45 level 0.3542
> transparency #45 50
> select add #45
2 models selected
> select add #44
4198 atoms, 4031 bonds, 8 pseudobonds, 743 residues, 4 models selected
> view matrix models
> #44,-0.93556,0.2937,-0.19611,146.23,0.044071,-0.45388,-0.88997,157.07,-0.3504,-0.84127,0.41169,60.574,#45,-0.93556,0.2937,-0.19611,146.23,0.044071,-0.45388,-0.88997,157.07,-0.3504,-0.84127,0.41169,60.574
> view matrix models
> #44,-0.93556,0.2937,-0.19611,143.48,0.044071,-0.45388,-0.88997,147.76,-0.3504,-0.84127,0.41169,34.922,#45,-0.93556,0.2937,-0.19611,143.48,0.044071,-0.45388,-0.88997,147.76,-0.3504,-0.84127,0.41169,34.922
> select subtract #45
4198 atoms, 4031 bonds, 8 pseudobonds, 743 residues, 2 models selected
> select subtract #44
Nothing selected
> hide #!44 models
> select add #45
2 models selected
> view matrix models
> #45,-0.93556,0.2937,-0.19611,145.49,0.044071,-0.45388,-0.88997,159.38,-0.3504,-0.84127,0.41169,39.151
> view matrix models
> #45,-0.72949,0.54043,-0.41926,144.13,0.020765,-0.59518,-0.80333,159.59,-0.68367,-0.59473,0.42296,41.013
> view matrix models
> #45,-0.71308,0.51521,-0.47548,145.84,0.057668,-0.6328,-0.77216,158.62,-0.69871,-0.57803,0.42153,41.063
> view matrix models
> #45,-0.71308,0.51521,-0.47548,145.43,0.057668,-0.6328,-0.77216,156.8,-0.69871,-0.57803,0.42153,40.9
> view matrix models
> #45,-0.71308,0.51521,-0.47548,145.15,0.057668,-0.6328,-0.77216,154.97,-0.69871,-0.57803,0.42153,40.73
> view matrix models
> #45,-0.79988,0.54237,-0.25694,140.06,-0.020652,-0.45275,-0.8914,156.94,-0.5998,-0.70771,0.37335,42.366
> select subtract #45
Nothing selected
> show #!44 models
> fitmap #44 inMap #45
Fit molecule copy of copy of AATHNEcombined (#44) to map copy of copy of
AATHNEcombined map 6 (#45) using 4198 atoms
average map value = 0.434, steps = 72
shifted from previous position = 8.8
rotated from previous position = 16.7 degrees
atoms outside contour = 994, contour level = 0.3542
Position of copy of copy of AATHNEcombined (#44) relative to copy of copy of
AATHNEcombined map 6 (#45) coordinates:
Matrix rotation and translation
0.99999987 0.00004904 -0.00050917 0.03695210
-0.00004923 0.99999993 -0.00038442 0.00896662
0.00050915 0.00038445 0.99999980 -0.01640243
Axis 0.60079207 -0.79570876 -0.07678841
Axis point 29.77463683 0.00000000 53.30306429
Rotation angle (degrees) 0.03666236
Shift along axis 0.01632523
> select add #44
4198 atoms, 4031 bonds, 8 pseudobonds, 743 residues, 2 models selected
> view matrix models
> #44,-0.80004,0.54224,-0.25675,156.75,-0.021083,-0.45309,-0.89121,165.09,-0.59958,-0.70759,0.37392,145.97
> view matrix models
> #44,-0.80004,0.54224,-0.25675,157.44,-0.021083,-0.45309,-0.89121,165.95,-0.59958,-0.70759,0.37392,150.1
> fitmap #44 inMap #29
Fit molecule copy of copy of AATHNEcombined (#44) to map J1122.mrc (#29) using
4198 atoms
average map value = 0.08149, steps = 152
shifted from previous position = 14.4
rotated from previous position = 16.8 degrees
atoms outside contour = 2047, contour level = 0.070992
Position of copy of copy of AATHNEcombined (#44) relative to J1122.mrc (#29)
coordinates:
Matrix rotation and translation
-0.93562730 0.29338154 -0.19628760 148.35386113
0.04432994 -0.45401135 -0.88989243 165.88171301
-0.35019481 -0.84130908 0.41177983 152.48885393
Axis 0.16370521 0.51860171 -0.83919775
Axis point 96.83079976 123.33491709 0.00000000
Rotation angle (degrees) 171.46655392
Shift along axis -17.65546343
> select subtract #44
Nothing selected
> select add #45
2 models selected
> view matrix models
> #45,-0.93329,0.27115,-0.23547,146.24,0.06955,-0.50681,-0.85925,155.22,-0.35232,-0.81831,0.45414,37.269
> select subtract #45
Nothing selected
> hide #!44 models
> open /Users/amy/Downloads/cryosparc_P483_J196_007_volume_map.mrc
Opened cryosparc_P483_J196_007_volume_map.mrc as #46, grid size 400,400,400,
pixel 0.723, shown at level 0.00453, step 2, values float32
> hide #!45 models
> hide #!43 models
> hide #!29 models
> hide #!8 models
> volume #46 level 0.03417
> open /Users/amy/Downloads/cryosparc_P483_J206_005_volume_map.mrc
Opened cryosparc_P483_J206_005_volume_map.mrc as #47, grid size 400,400,400,
pixel 0.723, shown at level 0.0164, step 2, values float32
> volume #47 level 0.05223
> volume #47 level 0.05304
> volume #47 level 0.05549
> close #58-61,70-71
> show #!46 models
> hide #!46 models
> close #46-47
> show #!39 models
Error processing trigger "graphics update":
You deleted or moved a volume file that is still open in ChimeraX.
/Users/amy/Downloads/cryosparc_P483_J188_006_volume_map.mrc
To allow fast initial display of volume data ChimeraX does not read all data
from the file when it is first opened, and will later read more data when
needed. ChimeraX got an error trying to read the above file.
> close #39-40
> save "/Users/amy/Desktop/SPA AAT_HNE/csparc.cxs"
——— End of log from Thu Mar 12 17:49:41 2026 ———
> view name session-start
opened ChimeraX session
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M5
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac17,2
Model Number: MDE64B/A
Chip: Apple M5
Total Number of Cores: 10 (4 Super and 6 Efficiency)
Memory: 24 GB
System Firmware Version: 13822.81.10
OS Loader Version: 13822.81.10
Software:
System Software Overview:
System Version: macOS 26.3.1 (a) (25D771280a)
Kernel Version: Darwin 25.3.0
Time since boot: 8天23分钟
Graphics/Displays:
Apple M5:
Chipset Model: Apple M5
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL P2314H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.1
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-ArtiaX: 0.6.0
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-Clipper: 0.26.1
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ISOLDE: 1.11.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
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: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.12
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
geomdl: 5.4.0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 25.0
pandas: 3.0.1
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pyarrow: 23.0.1
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
roman-numerals-py: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
sse-starlette: 3.2.0
stack-data: 0.6.3
starfile: 0.5.13
starlette: 0.52.1
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
urllib3: 2.6.3
uvicorn: 0.40.0
wcwidth: 0.3.2
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
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