![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 hours ago
#20383 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-26.4.1-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: Segmentation fault
Current thread 0x00000001ecbf98c0 (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, psutil._psutil_osx, psutil._psutil_posix, chimerax.map._map, 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, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, PIL._imagingmath, pyKVFinder._pyKVFinder, chimerax.mlp._mlp, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 56)
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"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
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"vmRegionInfo" : "0x8 is not in any region. Bytes before following region: 4365697016
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
__TEXT 104374000-104378000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000008","rawCodes":[1,8],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000008"},
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"vmregioninfo" : "0x8 is not in any region. Bytes before following region: 4365697016
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
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"name" : "libsystem_pthread.dylib"
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"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
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{
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Activity Tracing 256K 1
AttributeGraph Data 1024K 1
CG image 592K 20
ColorSync 144K 8
CoreAnimation 3152K 177
CoreGraphics 80K 5
CoreServices 704K 3
CoreUI image data 5856K 50
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Stack Guard 56.0M 1
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VM_ALLOCATE (reserved) 192.0M 1 reserved VM address space (unallocated)
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mapped file 659.0M 86
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shared memory 3200K 25
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===== Log before crash start =====
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/vatetaud/Downloads/pdb5ljo.ent format pdb
pdb5ljo.ent title:
E. Coli bam complex (bamabcde) by cryoem [more info...]
Chain information for pdb5ljo.ent #1
---
Chain | Description | UniProt
A | outer membrane protein assembly factor bama | BAMA_ECO45 24-806
B | outer membrane protein assembly factor bamb | BAMB_ECOLI 22-392
C | outer membrane protein assembly factor bamc | BAMC_ECOLI 25-189
D | outer membrane protein assembly factor bamd | BAMD_ECO57 26-243
E | outer membrane protein assembly factor bame | BAME_ECOL6 24-110
> hide #1 models
> set bgColor white
> open
> /Users/vatetaud/Desktop/Protein/OM_biogenesis/Lpt_bridge_vp/fold_lptfg_lpta_lptc_lptd_sp_vp_model_0.cif
Chain information for fold_lptfg_lpta_lptc_lptd_sp_vp_model_0.cif #2
---
Chain | Description
A | .
B | .
C | .
D | .
Computing secondary structure
> split #2
Split fold_lptfg_lpta_lptc_lptd_sp_vp_model_0.cif (#2) into 4 models
Chain information for fold_lptfg_lpta_lptc_lptd_sp_vp_model_0.cif A #2.1
---
Chain | Description
A | No description available
Chain information for fold_lptfg_lpta_lptc_lptd_sp_vp_model_0.cif B #2.2
---
Chain | Description
B | No description available
Chain information for fold_lptfg_lpta_lptc_lptd_sp_vp_model_0.cif C #2.3
---
Chain | Description
C | No description available
Chain information for fold_lptfg_lpta_lptc_lptd_sp_vp_model_0.cif D #2.4
---
Chain | Description
D | No description available
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.2 models
> hide #2.3 models
> hide #2.4 models
> select /A
14937 atoms, 15138 bonds, 1146 residues, 2 models selected
> show #2.2 models
> show #2.3 models
> show #2.4 models
> color (#2.1 & sel) #fffdeaff
> color (#2.1 & sel) #fffde9ff
> color (#2.1 & sel) #fffae7ff
> color (#2.1 & sel) #fff7e4ff
> color (#2.1 & sel) #fff3e1ff
> color (#2.1 & sel) #fff2e0ff
> color (#2.1 & sel) #fff1e0ff
> color (#2.1 & sel) #fff1dfff
> color (#2.1 & sel) #ffeedbff
> color (#2.1 & sel) #ffebd7ff
> color (#2.1 & sel) #ffe8d3ff
> color (#2.1 & sel) #ffe5d1ff
> color (#2.1 & sel) #ffe5d0ff
> color (#2.1 & sel) #ffe4cfff
> color (#2.1 & sel) #ffe2cdff
> color (#2.1 & sel) #ffdfcbff
> color (#2.1 & sel) #ffdac8ff
> color (#2.1 & sel) #ffd7c5ff
> color (#2.1 & sel) #ffd4c3ff
> color (#2.1 & sel) #ffd3c2ff
> color (#2.1 & sel) #ffd2c2ff
> color (#2.1 & sel) #ffd2c1ff
> color (#2.1 & sel) #ffd1c1ff
> color (#2.1 & sel) #ffc8bbff
> color (#2.1 & sel) #ffc1b8ff
> color (#2.1 & sel) #ffbbb4ff
> color (#2.1 & sel) #ffb8b3ff
> color (#2.1 & sel) #ffb6b2ff
> color (#2.1 & sel) #ffb7b1ff
> color (#2.1 & sel) #ffbab1ff
> color (#2.1 & sel) #ffbdb0ff
> color (#2.1 & sel) #ffc0b0ff
> color (#2.1 & sel) #ffc4afff
> color (#2.1 & sel) #ffc5afff
> color (#2.1 & sel) #ffc6afff
> color (#2.1 & sel) #ffc7b0ff
> color (#2.1 & sel) #ffc9b0ff
> color (#2.1 & sel) #ffcab1ff
> color (#2.1 & sel) #ffcbb2ff
> color (#2.1 & sel) #ffceb4ff
> color (#2.1 & sel) #ffd2b7ff
> color (#2.1 & sel) #ffd8bbff
> color (#2.1 & sel) #ffe2c2ff
> color (#2.1 & sel) #ffe5c6ff
> color (#2.1 & sel) #ffe7c7ff
> color (#2.1 & sel) #ffe6c9ff
> color (#2.1 & sel) #ffe3cbff
> color (#2.1 & sel) #ffe1ccff
> color (#2.1 & sel) #ffdfceff
> color (#2.1 & sel) #ffdccfff
> color (#2.1 & sel) #ffdbcfff
> color (#2.1 & sel) #ffdacfff
> color (#2.1 & sel) #ffd9cfff
> color (#2.1 & sel) #ffd8cfff
> color (#2.1 & sel) #ffd6d0ff
> color (#2.1 & sel) #ffd5d0ff
> color (#2.1 & sel) #ffd3d0ff
> color (#2.1 & sel) #ffd1cfff
> color (#2.1 & sel) #ffcfcfff
> color (#2.1 & sel) #ffcfd1ff
> color (#2.1 & sel) #ffced1ff
> color (#2.1 & sel) #ffced2ff
> color (#2.1 & sel) #ffcdd4ff
> color (#2.1 & sel) #ffcdd6ff
> color (#2.1 & sel) #ffccdaff
> color (#2.1 & sel) #ffcbdcff
> color (#2.1 & sel) #ffcaddff
> color (#2.1 & sel) #ffcbdfff
> color (#2.1 & sel) #ffd4e2ff
> color (#2.1 & sel) #ffd9e4ff
> color (#2.1 & sel) #ffdce4ff
> color (#2.1 & sel) #ffdee5ff
> color (#2.1 & sel) #ffdde4ff
> color (#2.1 & sel) #ffdce4ff
> color (#2.1 & sel) #ffdce3ff
> color (#2.1 & sel) #ffdbe2ff
> color (#2.1 & sel) #ffdae2ff
> color (#2.1 & sel) #ffd8dfff
> color (#2.1 & sel) #ffd6dcff
> color (#2.1 & sel) #ffd3d9ff
> color (#2.1 & sel) #ffd2d7ff
> color (#2.1 & sel) #ffd1d6ff
> color (#2.1 & sel) #ffd1d5ff
> color (#2.1 & sel) #ffd0d4ff
> color (#2.1 & sel) #ffcfd1ff
> color (#2.1 & sel) #ffcdceff
> color (#2.1 & sel) #ffcccbff
> color (#2.1 & sel) #ffcccaff
> color (#2.1 & sel) #ffccc9ff
> color (#2.1 & sel) #ffccc8ff
> color (#2.1 & sel) #ffccc6ff
> color (#2.1 & sel) #ffccc3ff
> color (#2.1 & sel) #ffcdc3ff
> color (#2.1 & sel) #ffccc3ff
> color (#2.1 & sel) #ffccc4ff
> color (#2.1 & sel) #ffccc5ff
> color (#2.1 & sel) #ffccc6ff
> color (#2.1 & sel) #ffccc8ff
> color (#2.1 & sel) #ffcdc9ff
> color (#2.1 & sel) #ffcdcaff
> color (#2.1 & sel) #ffcdccff
> color (#2.1 & sel) #ffceccff
> color (#2.1 & sel) #ffcfccff
> color (#2.1 & sel) #ffd1ccff
> color (#2.1 & sel) #ffd3cbff
> color (#2.1 & sel) #ffd5cbff
> color (#2.1 & sel) #ffd6cbff
> color (#2.1 & sel) #ffd7cbff
> color (#2.1 & sel) #ffd6cbff
> color (#2.1 & sel) #ffd7cbff
> color (#2.1 & sel) #ffd7caff
> color (#2.1 & sel) #ffd8caff
> select /B
7125 atoms, 7196 bonds, 586 residues, 2 models selected
> select /C
3865 atoms, 3904 bonds, 343 residues, 2 models selected
> color (#2.3 & sel) #ffb4b4ff
> color (#2.3 & sel) #ffb6b6ff
> color (#2.3 & sel) #ffb7b8ff
> color (#2.3 & sel) #ffb9bbff
> color (#2.3 & sel) #ffbbbdff
> color (#2.3 & sel) #ffbcbfff
> color (#2.3 & sel) #ffbcc0ff
> color (#2.3 & sel) #ffbcc1ff
> color (#2.3 & sel) #ffbcc2ff
> color (#2.3 & sel) #ffbcc3ff
> color (#2.3 & sel) #ffbdc5ff
> color (#2.3 & sel) #ffbec8ff
> color (#2.3 & sel) #ffbecaff
> color (#2.3 & sel) #ffbfcbff
> color (#2.3 & sel) #ffbfccff
> color (#2.3 & sel) #ffbfcdff
> color (#2.3 & sel) #ffc0ceff
> color (#2.3 & sel) #ffc0d0ff
> color (#2.3 & sel) #ffc1d1ff
> color (#2.3 & sel) #ffc1d2ff
> color (#2.3 & sel) #ffc1d3ff
> color (#2.3 & sel) #ffc1d4ff
> color (#2.3 & sel) #ffc2d6ff
> color (#2.3 & sel) #ffc2d8ff
> color (#2.3 & sel) #ffc3daff
> color (#2.3 & sel) #ffc3dcff
> color (#2.3 & sel) #ffc3ddff
> color (#2.3 & sel) #ffc2deff
> color (#2.3 & sel) #ffc1ddff
> color (#2.3 & sel) #ffc0ddff
> color (#2.3 & sel) #ffbfddff
> color (#2.3 & sel) #ffbedcff
> color (#2.3 & sel) #ffbdddff
> color (#2.3 & sel) #ffbcdeff
> color (#2.3 & sel) #ffbbdfff
> color (#2.3 & sel) #ffbae0ff
> color (#2.3 & sel) #ffb9e1ff
> color (#2.3 & sel) #ffb9e2ff
> color (#2.3 & sel) #ffb8e2ff
> color (#2.3 & sel) #ffb7e3ff
> color (#2.3 & sel) #ffb6e4ff
> color (#2.3 & sel) #ffb7e3ff
> color (#2.3 & sel) #ffb8e2ff
> color (#2.3 & sel) #ffb9e2ff
> color (#2.3 & sel) #ffb9e3ff
> color (#2.3 & sel) #ffb9e4ff
> color (#2.3 & sel) #ffb9e6ff
> color (#2.3 & sel) #ffb9e7ff
> color (#2.3 & sel) #ffb9e8ff
> color (#2.3 & sel) #ffb8e9ff
> color (#2.3 & sel) #ffb9eaff
> color (#2.3 & sel) #ffbaebff
> color (#2.3 & sel) #ffbaecff
> color (#2.3 & sel) #ffbbedff
> color (#2.3 & sel) #ffbceeff
> color (#2.3 & sel) #ffbef0ff
> color (#2.3 & sel) #ffbff1ff
> color (#2.3 & sel) #ffbff2ff
> select /B
7125 atoms, 7196 bonds, 586 residues, 2 models selected
> color (#2.2 & sel) #ffccfcff
> color (#2.2 & sel) #ffcdfcff
> color (#2.2 & sel) #ffcefeff
> color (#2.2 & sel) #fccfffff
> color (#2.2 & sel) #f6cfffff
> color (#2.2 & sel) #f0cdffff
> color (#2.2 & sel) #eaccffff
> color (#2.2 & sel) #e7caffff
> color (#2.2 & sel) #e5c9ffff
> color (#2.2 & sel) #e3c9ffff
> color (#2.2 & sel) #e2c9ffff
> color (#2.2 & sel) #e0c9ffff
> color (#2.2 & sel) #ddc8ffff
> color (#2.2 & sel) #d7c6ffff
> color (#2.2 & sel) #d0c3ffff
> color (#2.2 & sel) #cbc1ffff
> color (#2.2 & sel) #c5bfffff
> color (#2.2 & sel) #c4bfffff
> color (#2.2 & sel) #c3beffff
> color (#2.2 & sel) #c2beffff
> color (#2.2 & sel) #c1beffff
> color (#2.2 & sel) #bfbeffff
> select /D
7427 atoms, 7573 bonds, 712 residues, 2 models selected
> color (#2.4 & sel) #d1d0ffff
> color (#2.4 & sel) #d1d2ffff
> color (#2.4 & sel) #d1d4ffff
> color (#2.4 & sel) #d1d6ffff
> color (#2.4 & sel) #d1d7ffff
> color (#2.4 & sel) #d1d8ffff
> color (#2.4 & sel) #d2d9ffff
> color (#2.4 & sel) #d2daffff
> color (#2.4 & sel) #d3dbffff
> color (#2.4 & sel) #d2ddffff
> color (#2.4 & sel) #d2deffff
> color (#2.4 & sel) #d2dfffff
> color (#2.4 & sel) #d2e0ffff
> color (#2.4 & sel) #d2e1ffff
> color (#2.4 & sel) #d2e4ffff
> color (#2.4 & sel) #d2e5ffff
> color (#2.4 & sel) #d2e7ffff
> color (#2.4 & sel) #d2e8ffff
> color (#2.4 & sel) #d2e9ffff
> color (#2.4 & sel) #d2eaffff
> color (#2.4 & sel) #d2ebffff
> color (#2.4 & sel) #d2ecffff
> color (#2.4 & sel) #d1edffff
> color (#2.4 & sel) #d1efffff
> color (#2.4 & sel) #d0f2ffff
> color (#2.4 & sel) #cff3ffff
> color (#2.4 & sel) #cff4ffff
> color (#2.4 & sel) #cef4ffff
> color (#2.4 & sel) #cef5ffff
> color (#2.4 & sel) #cdf7ffff
> color (#2.4 & sel) #ccf9ffff
> color (#2.4 & sel) #cbfbffff
> color (#2.4 & sel) #cafdffff
> color (#2.4 & sel) #cafeffff
> color (#2.4 & sel) #c9feffff
> color (#2.4 & sel) #c7ffffff
> color (#2.4 & sel) #c6ffffff
> select clear
> show #2.1-4 surfaces
> save /Users/vatetaud/Desktop/image8.png supersample 3
> hide #!2 models
> open
> /Users/vatetaud/Desktop/Protein/TIM/fold_lptd_petit_43595_hsaccharolyticum/fold_lptd_petit_43595_hsaccharolyticum_model_0.cif
Chain information for fold_lptd_petit_43595_hsaccharolyticum_model_0.cif #3
---
Chain | Description
A | .
Computing secondary structure
> hide #3 models
> hide #!2.4 models
> hide #!2.3 models
> hide #!2.2 models
> show #!2 models
> hide #!2.1 models
> show #!2.4 models
> hide #!2.4 surfaces
> select /D
7427 atoms, 7573 bonds, 712 residues, 2 models selected
> color (#!2.4 & sel) #a7fff6ff
> color (#!2.4 & sel) #a7fff9ff
> color (#!2.4 & sel) #a8ffffff
> color (#!2.4 & sel) #a5eaffff
> color (#!2.4 & sel) #a4e7ffff
> color (#!2.4 & sel) #a2e0ffff
> color (#!2.4 & sel) #a1ddffff
> color (#!2.4 & sel) #a0dbffff
> color (#!2.4 & sel) #9fd8ffff
> color (#!2.4 & sel) #9fd7ffff
> color (#!2.4 & sel) #9ed6ffff
> color (#!2.4 & sel) #9dd4ffff
> color (#!2.4 & sel) #9cd3ffff
> color (#!2.4 & sel) #9acfffff
> color (#!2.4 & sel) #99ceffff
> color (#!2.4 & sel) #97ccffff
> color (#!2.4 & sel) #94c8ffff
> color (#!2.4 & sel) #8abeffff
> color (#!2.4 & sel) #87bbffff
> color (#!2.4 & sel) #84b8ffff
> color (#!2.4 & sel) #83b6ffff
> color (#!2.4 & sel) #82b5ffff
> color (#!2.4 & sel) #81b3ffff
> color (#!2.4 & sel) #7faeffff
> color (#!2.4 & sel) #7daaffff
> color (#!2.4 & sel) #7aa2ffff
> color (#!2.4 & sel) #789effff
> color (#!2.4 & sel) #779cffff
> color (#!2.4 & sel) #779affff
> color (#!2.4 & sel) #789affff
> color (#!2.4 & sel) #7899ffff
> color (#!2.4 & sel) #7395ffff
> color (#!2.4 & sel) #6f91ffff
> color (#!2.4 & sel) #6c8dffff
> color (#!2.4 & sel) #698bffff
> color (#!2.4 & sel) #688affff
> color (#!2.4 & sel) #678affff
> color (#!2.4 & sel) #668affff
> color (#!2.4 & sel) #658affff
> color (#!2.4 & sel) #658bffff
> color (#!2.4 & sel) #658dffff
> color (#!2.4 & sel) #648fffff
> color (#!2.4 & sel) #6490ffff
> color (#!2.4 & sel) #6591ffff
> color (#!2.4 & sel) #6592ffff
> color (#!2.4 & sel) #6694ffff
> color (#!2.4 & sel) #6795ffff
> color (#!2.4 & sel) #6896ffff
> color (#!2.4 & sel) #6997ffff
> color (#!2.4 & sel) #6a98ffff
> color (#!2.4 & sel) #6b99ffff
> color (#!2.4 & sel) #6c9affff
> color (#!2.4 & sel) #6d9affff
> color (#!2.4 & sel) #6e9cffff
> color (#!2.4 & sel) #709dffff
> color (#!2.4 & sel) #709effff
> color (#!2.4 & sel) #719fffff
> color (#!2.4 & sel) #72a0ffff
> color (#!2.4 & sel) #74a1ffff
> color (#!2.4 & sel) #75a2ffff
> color (#!2.4 & sel) #77a4ffff
> color (#!2.4 & sel) #76a3ffff
> color (#!2.4 & sel) #76a2ffff
> color (#!2.4 & sel) #75a1ffff
> color (#!2.4 & sel) #749fffff
> color (#!2.4 & sel) #739effff
> color (#!2.4 & sel) #719dffff
> color (#!2.4 & sel) #6f9dffff
> color (#!2.4 & sel) #6d9dffff
> color (#!2.4 & sel) #6d9cffff
> color (#!2.4 & sel) #6c9cffff
> color (#!2.4 & sel) #6b9bffff
> color (#!2.4 & sel) #6a9bffff
> color (#!2.4 & sel) #679bffff
> color (#!2.4 & sel) #669bffff
> color (#!2.4 & sel) #659bffff
> color (#!2.4 & sel) #659affff
> color (#!2.4 & sel) #649affff
> color (#!2.4 & sel) #6299ffff
> color (#!2.4 & sel) #6198ffff
> color (#!2.4 & sel) #6097ffff
> color (#!2.4 & sel) #5f97ffff
> color (#!2.4 & sel) #5d95ffff
> color (#!2.4 & sel) #5c94ffff
> color (#!2.4 & sel) #5b93ffff
> color (#!2.4 & sel) #5a92ffff
> color (#!2.4 & sel) #5991ffff
> select clear
> select #2.4/D:227
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #2.4/D:226
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /D:44-226
4373 atoms, 4441 bonds, 366 residues, 2 models selected
> color (#!2.4 & sel) #76acffff
> color (#!2.4 & sel) #75acffff
> color (#!2.4 & sel) #76acffff
> color (#!2.4 & sel) #77acffff
> color (#!2.4 & sel) #78abffff
> color (#!2.4 & sel) #79abffff
> color (#!2.4 & sel) #79aaffff
> color (#!2.4 & sel) #79a6ffff
> color (#!2.4 & sel) #779bffff
> color (#!2.4 & sel) #7695ffff
> color (#!2.4 & sel) #7591ffff
> color (#!2.4 & sel) #738dffff
> color (#!2.4 & sel) #7289ffff
> color (#!2.4 & sel) #7185ffff
> color (#!2.4 & sel) #7082ffff
> color (#!2.4 & sel) #6f7fffff
> color (#!2.4 & sel) #6e7bffff
> color (#!2.4 & sel) #6e79ffff
> color (#!2.4 & sel) #6e76ffff
> color (#!2.4 & sel) #6d74ffff
> color (#!2.4 & sel) #6d71ffff
> color (#!2.4 & sel) #6e6fffff
> color (#!2.4 & sel) #706effff
> color (#!2.4 & sel) #766fffff
> color (#!2.4 & sel) #7d70ffff
> color (#!2.4 & sel) #8371ffff
> color (#!2.4 & sel) #9073ffff
> color (#!2.4 & sel) #9473ffff
> color (#!2.4 & sel) #9873ffff
> color (#!2.4 & sel) #9a72ffff
> color (#!2.4 & sel) #9e71ffff
> color (#!2.4 & sel) #9f71ffff
> color (#!2.4 & sel) #a171ffff
> color (#!2.4 & sel) #a372ffff
> color (#!2.4 & sel) #a572ffff
> color (#!2.4 & sel) #a872ffff
> color (#!2.4 & sel) #ab73ffff
> color (#!2.4 & sel) #af72ffff
> color (#!2.4 & sel) #b271ffff
> color (#!2.4 & sel) #b770ffff
> color (#!2.4 & sel) #ba6effff
> color (#!2.4 & sel) #bd6dffff
> color (#!2.4 & sel) #bf6cffff
> color (#!2.4 & sel) #c26cffff
> color (#!2.4 & sel) #c16cffff
> color (#!2.4 & sel) #c06cffff
> color (#!2.4 & sel) #bf6bffff
> color (#!2.4 & sel) #bd6affff
> color (#!2.4 & sel) #b969ffff
> color (#!2.4 & sel) #b369ffff
> color (#!2.4 & sel) #ad68ffff
> color (#!2.4 & sel) #a867ffff
> color (#!2.4 & sel) #a567ffff
> color (#!2.4 & sel) #a367ffff
> color (#!2.4 & sel) #a267ffff
> color (#!2.4 & sel) #a167ffff
> color (#!2.4 & sel) #a066ffff
> color (#!2.4 & sel) #9e66ffff
> color (#!2.4 & sel) #9d65ffff
> color (#!2.4 & sel) #9b64ffff
> color (#!2.4 & sel) #9a63ffff
> color (#!2.4 & sel) #9963ffff
> color (#!2.4 & sel) #9962ffff
> color (#!2.4 & sel) #9862ffff
> color (#!2.4 & sel) #9762ffff
> color (#!2.4 & sel) #9662ffff
> select clear
> save /Users/vatetaud/Desktop/image9.png supersample 3
> hide #!2.4 models
> show #3 models
> select clear
Drag select of 1 residues
> select #3/A:591
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #3:209-591
3217 atoms, 3305 bonds, 383 residues, 1 model selected
> color (#!2.4 & sel) #5991ffff
> color (#!2.4 & sel) #5991ffff selectedOnly
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color (#!2.4 & sel) #5991ffff SelectedOnly
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color SelectedOnly #5991ffff
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #5991ffff
> color #5991ffff selectedOnly
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #5991ffff selectedo\nly
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #5991ffff selectedonly
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #5991ffff select
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel #5991ffff
> close #3
> open
> /Users/vatetaud/Desktop/Protein/TIM/LptD/fold_lptd_petit_sp_43595_hsaccharolyticum/fold_lptd_petit_sp_43595_hsaccharolyticum_model_0.cif
Chain information for fold_lptd_petit_sp_43595_hsaccharolyticum_model_0.cif #3
---
Chain | Description
A | .
Computing secondary structure
> select #3/A:178
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #3:37-208
1375 atoms, 1411 bonds, 172 residues, 1 model selected
> select #3:37-208
1375 atoms, 1411 bonds, 172 residues, 1 model selected
> select #3:178-557
3192 atoms, 3278 bonds, 380 residues, 1 model selected
> color sel #9662ffff
> select clear
> select #3/A:178
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3:178-557
3192 atoms, 3278 bonds, 380 residues, 1 model selected
> color sel #9662ffff
> select :1-177
17585 atoms, 17812 bonds, 1587 residues, 6 models selected
> color sel #5991ffff
> color sel #9662ffff
> select #3:178-557
3192 atoms, 3278 bonds, 380 residues, 1 model selected
> color sel #5991ffff
> select clear
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2.4 models
> hide #!2.4 models
> show #!2.4 models
> hide #!2.4 models
> save /Users/vatetaud/Desktop/image10.png supersample 3
> hide #3 models
> show #!2.4 models
> save /Users/vatetaud/Desktop/image11.png supersample 3
> hide #!2.4 models
> open
> /Users/vatetaud/Desktop/Protein/TIM/LptD/fold_lptd_grand_sp_43595_hsaccharolyticum/fold_lptd_grand_sp_43595_hsaccharolyticum_model_0.cif
Chain information for fold_lptd_grand_sp_43595_hsaccharolyticum_model_0.cif #4
---
Chain | Description
A | .
Computing secondary structure
> select #4/A:343
14 atoms, 15 bonds, 1 residue, 1 model selected
> shape rectangle width 80 height 80 color lightblue modelId #10
> shape rectangle width 80 height 80 Thickness 80color lightblue modelId #10
Expected a keyword
> shape rectangle width 80 height 80 Thickness 80 color lightblue modelId #10
Expected a keyword
> shape rectangle width 80 height 80 Thick 80 color lightblue modelId #10
Expected a keyword
> shape rectangle width 80 height 80 thick 80 color lightblue modelId #10
Expected a keyword
> shape rectangle width 80 height 80 thickness 80 color lightblue modelId #10
Expected a keyword
> hide #4 models
> moove z 60 #10
Unknown command: moove z 60 #10
> move z 60 #10
Expected an integer >= 1 or a keyword
> move z 60 models #10
> show #4 models
> hide #10 models
> break 343@N 344@C
Unknown command: break 343@N 344@C
> delete bound: 343@C 344@N
Missing or invalid "atoms" argument: invalid atoms specifier
> delete bound: 343@C 344@N
Missing or invalid "atoms" argument: invalid atoms specifier
> delete bond: 343@C 344@N
Missing or invalid "atoms" argument: invalid atoms specifier
> delete bond: 343@C :344@N
Missing or invalid "atoms" argument: invalid atoms specifier
> delete bonds :250@C :251@N
> undo
> hide #10 models
> hide #4.1 models
> close #4.1
> select :250
65 atoms, 60 bonds, 6 residues, 5 models selected
> select :250-260
701 atoms, 697 bonds, 5 pseudobonds, 66 residues, 9 models selected
> select clear
> select #4/A:343
14 atoms, 15 bonds, 1 residue, 1 model selected
> delete bonds :343@C :344@N
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> split #4
Did not split fold_lptd_grand_sp_43595_hsaccharolyticum_model_0.cif, has only
one piece
> hide #4.1 models
> select clear
> open
> /Users/vatetaud/Desktop/Protein/TIM/LptD/fold_lptd_grand_sp_43595_hsaccharolyticum/fold_lptd_grand_sp_43595_hsaccharolyticum_model_1.cif
> /Users/vatetaud/Desktop/Protein/TIM/LptD/fold_lptd_grand_sp_43595_hsaccharolyticum/fold_lptd_grand_sp_43595_hsaccharolyticum_model_2.cif
> /Users/vatetaud/Desktop/Protein/TIM/LptD/fold_lptd_grand_sp_43595_hsaccharolyticum/fold_lptd_grand_sp_43595_hsaccharolyticum_model_3.cif
> /Users/vatetaud/Desktop/Protein/TIM/LptD/fold_lptd_grand_sp_43595_hsaccharolyticum/fold_lptd_grand_sp_43595_hsaccharolyticum_model_4.cif
Chain information for fold_lptd_grand_sp_43595_hsaccharolyticum_model_1.cif #5
---
Chain | Description
A | .
Chain information for fold_lptd_grand_sp_43595_hsaccharolyticum_model_2.cif #6
---
Chain | Description
A | .
Chain information for fold_lptd_grand_sp_43595_hsaccharolyticum_model_3.cif #7
---
Chain | Description
A | .
Chain information for fold_lptd_grand_sp_43595_hsaccharolyticum_model_4.cif #8
---
Chain | Description
A | .
Computing secondary structure
> hide #8 models
> hide #7 models
> hide #6 models
> hide #!4 models
> show #6 models
> hide #5 models
> show #7 models
> hide #6 models
> show #8 models
> hide #7 models
> close #5-7
> hide #8 models
> close #8
> show #!4 models
> select #4/A:248
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #4/A:250
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #4/A:251
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/A:342
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #4/A:343
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #4/A:344
11 atoms, 10 bonds, 1 residue, 1 model selected
> delete bonds :343@C :344@N
> select clear
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> close #4
> open
> /Users/vatetaud/Desktop/Protein/TIM/LptD/fold_lptd_grand_sp_43595_hsaccharolyticum/fold_lptd_grand_sp_43595_hsaccharolyticum_model_0.cif
Chain information for fold_lptd_grand_sp_43595_hsaccharolyticum_model_0.cif #4
---
Chain | Description
A | .
Computing secondary structure
> delete bonds :343@C :344@N
> split #4
Did not split fold_lptd_grand_sp_43595_hsaccharolyticum_model_0.cif, has only
one piece
> select add #4.1
1 pseudobond, 1 model selected
> select subtract #4.1
Nothing selected
> select add #10
1 model selected
> select subtract #10
Nothing selected
> select add #4.1
1 pseudobond, 1 model selected
> select up
8793 atoms, 9015 bonds, 1 pseudobond, 1056 residues, 2 models selected
> select down
1 pseudobond, 1 model selected
> select up
8793 atoms, 9015 bonds, 1 pseudobond, 1056 residues, 2 models selected
> select down
1 pseudobond, 1 model selected
> select up
8793 atoms, 9015 bonds, 1 pseudobond, 1056 residues, 2 models selected
> select down
1 pseudobond, 1 model selected
> select down
1 pseudobond, 1 model selected
> delete bonds :343@C :344@N
> select ~sel & ##selected
1 pseudobond, 1 model selected
> show #!1 models
> hide #!1 models
> delete bonds #4:343@C :344@N
> select #4 /a
8793 atoms, 9015 bonds, 1 pseudobond, 1056 residues, 2 models selected
> select #4 /A
8793 atoms, 9015 bonds, 1 pseudobond, 1056 residues, 2 models selected
> delete bonds :343@C :344@N
> select up
8793 atoms, 9015 bonds, 1 pseudobond, 1056 residues, 2 models selected
> select up
38337 atoms, 38948 bonds, 1 pseudobond, 3237 residues, 6 models selected
> select up
38337 atoms, 38948 bonds, 1 pseudobond, 3237 residues, 6 models selected
> delete bonds :343@C :344@N
> select clear
> move z 60
> select : 1-343
31020 atoms, 31462 bonds, 5 pseudobonds, 2877 residues, 11 models selected
> hide #!2 models
> select add #3
32809 atoms, 33302 bonds, 6 pseudobonds, 3091 residues, 15 models selected
> select add #2.4
34079 atoms, 34609 bonds, 7 pseudobonds, 3242 residues, 15 models selected
> select subtract #3
29482 atoms, 29892 bonds, 5 pseudobonds, 2685 residues, 13 models selected
> select subtract #2.4
25516 atoms, 25822 bonds, 3 pseudobonds, 2191 residues, 11 models selected
> select add #2
29641 atoms, 30054 bonds, 6 pseudobonds, 2705 residues, 13 models selected
> select subtract #2
19882 atoms, 20100 bonds, 2 pseudobonds, 1455 residues, 7 models selected
> select add #1
27703 atoms, 28031 bonds, 4 pseudobonds, 1967 residues, 3 models selected
> select subtract #1
2756 atoms, 2815 bonds, 343 residues, 1 model selected
> turn y 90 models #4
> delete bonds #4 :343@C :344@N
> select clear
> delete bonds #4 :250@C :251@N
> select :250-260
701 atoms, 697 bonds, 6 pseudobonds, 66 residues, 10 models selected
> select add #1
25307 atoms, 25573 bonds, 8 pseudobonds, 1668 residues, 12 models selected
> select subtract #1
360 atoms, 357 bonds, 4 pseudobonds, 44 residues, 10 models selected
> select add #2
9936 atoms, 10128 bonds, 6 pseudobonds, 1272 residues, 13 models selected
> select subtract #2
177 atoms, 174 bonds, 2 pseudobonds, 22 residues, 8 models selected
> delete bonds #4 :250@C :251@N
> hide #4.1 models
> select clear
> select add #4.1
2 pseudobonds, 1 model selected
> select subtract #4.1
Nothing selected
> select add #4.1
2 pseudobonds, 1 model selected
> select subtract #4.1
Nothing selected
> select add #4.1
2 pseudobonds, 1 model selected
> select subtract #4.1
Nothing selected
> select add #4.1
2 pseudobonds, 1 model selected
> select subtract #4.1
Nothing selected
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> delete bonds :250@C :251@N
> move x 30 models #4
> move z 50 models #4
> ui mousemode right "tape measure"
> ui mousemode right "move planes"
> ui mousemode right "rotate slab"
> ui tool show Distances
> select #4/A:82
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 4 atom styles
> hide sel cartoons
> select clear
> select #4/A:82@O
1 atom, 1 residue, 1 model selected
> select #4/A:203
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #4/A:203@OE1
1 atom, 1 residue, 1 model selected
> select add #4/A:82@O
2 atoms, 2 residues, 1 model selected
> distance #4/A:203@OE1 #4/A:82@O
Distance between fold_lptd_grand_sp_43595_hsaccharolyticum_model_0.cif #4/A
GLN 203 OE1 and GLY 82 O: 90.213Å
> select #4/A:393
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #4/A:1026
14 atoms, 12 bonds, 2 residues, 1 model selected
> show sel atoms
> select clear
> select #4/A:393@OG
1 atom, 1 residue, 1 model selected
> select add #4/A:1026@CD1
2 atoms, 2 residues, 1 model selected
> distance #4/A:393@OG #4/A:1026@CD1
Distance between fold_lptd_grand_sp_43595_hsaccharolyticum_model_0.cif #4/A
SER 393 OG and LEU 1026 CD1: 28.809Å
> select #4/A:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #4/A:157@NZ
1 atom, 1 residue, 1 model selected
> select clear
> select #4/A:157@NZ
1 atom, 1 residue, 1 model selected
> select add #4/A:203@CD
2 atoms, 1 bond, 2 residues, 1 model selected
> select add #4/A:203@OE1
3 atoms, 2 residues, 1 model selected
Exactly two atoms must be selected!
> select clear
> select #4/A:203@OE1
1 atom, 1 residue, 1 model selected
> select add #4/A:157@NZ
2 atoms, 2 residues, 1 model selected
> distance #4/A:203@OE1 #4/A:157@NZ
Distance between fold_lptd_grand_sp_43595_hsaccharolyticum_model_0.cif #4/A
GLN 203 OE1 and LYS 157 NZ: 47.913Å
> show #!2 models
> show #!2.1 models
> show #!2.2 models
> show #!2.3 models
> show #!2.4 models
> hide #!4 models
> select all
48096 atoms, 48901 bonds, 15 pseudobonds, 4487 residues, 16 models selected
> hide sel & #!2.1-4 surfaces
> select clear
> hide #!2 models
> show #!2 models
> select #2.1/A:153
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #2.4/D:227
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #2.4/D:227@CD1
1 atom, 1 residue, 1 model selected
> select add #2.1/A:153@NZ
2 atoms, 2 residues, 3 models selected
> distance #2.4/D:227@CD1 #2.1/A:153@NZ
Distance between fold_lptfg_lpta_lptc_lptd_sp_vp_model_0.cif D #2.4/D ILE 227
CD1 and fold_lptfg_lpta_lptc_lptd_sp_vp_model_0.cif A #2.1/A LYS 153 NZ:
159.382Å
> ~distance #4/A:203@OE1 #4/A:82@O
> show #!4 models
> distance style color #fa1104
> distance style color #790802
> distance style color #780802
> distance style color #770802
> distance style color #710802
> distance style color #6d0802
> distance style color #680702
> distance style color #630701
> distance style color #5e0701
> distance style color #580601
> distance style color #530601
> distance style color #440501
> distance style color #3d0401
> distance style color #350401
> distance style color #270301
> distance style color #1a0200
> distance style color #160200
> distance style color #100100
> distance style color #0e0100
> distance style color #0d0100
> distance style color #0c0100
> distance style color #0a0100
> distance style color #050000
> distance style color #020000
> distance style color black
> distance style color #0a0100
> distance style color #1c0200
> distance style color #250301
> distance style color #2c0301
> distance style color #330401
> distance style color #3d0401
> distance style color #430501
> distance style color #460501
> distance style color #490501
> distance style color #4c0501
> distance style color #4e0501
> distance style color #520601
> distance style color #540601
> distance style color #550601
> distance style color #560601
> distance style color #570601
> distance style color #590601
> distance style color #600701
> distance style color #650701
> distance style color #680702
> distance style color #6b0802
> distance style color #6e0802
> distance style color #730802
> distance style color #760802
> distance style color #790802
> distance style color #7d0902
> distance style color #810902
> distance style color #850902
> distance style color #920a02
> distance style color #9a0b02
> distance style color #a20b02
> distance style color #b20c03
> distance style color #ba0d03
> distance style color #c10d03
> distance style color #ce0e03
> distance style color #d30f03
> hide #!4 models
> show #!4 models
> hide #!2 models
> select #4/A:377
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #4/A:376
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/A:377
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #4/A:376
11 atoms, 9 bonds, 2 residues, 1 model selected
> ui mousemode right rotate
> ui mousemode right select
> ui mousemode right pivot
Drag select of 1 residues
> select #4/A:375
4 atoms, 3 bonds, 1 residue, 1 model selected
Drag select of 1 residues
> ui tool show "Find Cavities"
pyKVFinder module not installed; fetching from PyPi repository...
Errors may have occurred when running pip:
pip standard error:
\---
ERROR: pip's dependency resolver does not currently take into account all the
packages that are installed. This behaviour is the source of the following
dependency conflicts.
nptyping 2.5.0 requires numpy=1.20.0; python_version >= "3.8", but you
have numpy 2.4.6 which is incompatible.
scipy 1.14.0 requires numpy=1.23.5, but you have numpy 2.4.6 which is
incompatible.
\---
pip standard output:
\---
\---
pyKVFinder module installed from PyPi repository.
> hide sel atoms
> show sel cartoons
> select clear
> ui tool show Rotamers
Populating font family aliases took 52 ms. Replace uses of missing font family
"Times" with one that exists to avoid this cost.
> select #4/A:493
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide #!2.1 models
> hide #!2.2 models
> hide #!2.3 models
> hide #!2.4 models
> select clear
> select #4/A:1056
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/A:493-1056
4825 atoms, 4959 bonds, 564 residues, 1 model selected
> color sel #5991ffff
> select up
4833 atoms, 4967 bonds, 565 residues, 1 model selected
> select clear
> select #4/A:377
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #4/A:377-492
955 atoms, 979 bonds, 116 residues, 1 model selected
> color sel 9662ffff
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel #9662ffff
> select clear
> select #4/A:157@CE
1 atom, 1 residue, 1 model selected
> show sel cartoons
> hide sel atoms
> select #4/A:157@CD
1 atom, 1 residue, 1 model selected
> hide #5.1 models
> show #5.1 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> select #4/A:157@NZ
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #4/A:157
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #4/A:203
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #4/A:220
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #4/A:133
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:133-220
740 atoms, 756 bonds, 1 pseudobond, 88 residues, 2 models selected
> color sel #9662ffff
> select #4/A:794
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #4/A:376
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> select #4/A:359
4 atoms, 3 bonds, 1 residue, 1 model selected
> select clear
> select #4/A:221
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:221-359
1121 atoms, 1144 bonds, 2 pseudobonds, 139 residues, 2 models selected
> distance style color #d31409
> distance style color #d3160b
> distance style color #d31b14
> distance style color #d32424
> distance style color #d33640
> distance style color #d3495d
> distance style color #d35976
> distance style color #d3688a
> distance style color #d3749b
> distance style color #d37da8
> distance style color #d383b0
> distance style color #d386b5
> distance style color #d387b7
> distance style color #d386b7
> distance style color #d386b6
> distance style color #d385b5
> distance style color #d384b4
> distance style color #d383b3
> distance style color #d382b2
> distance style color #d381b1
> distance style color #d380b2
> distance style color #d37fb2
> distance style color #d37db3
> distance style color #d379b6
> distance style color #d374b9
> distance style color #d36dbe
> distance style color #d367c4
> distance style color #d362cb
> distance style color #d360d0
> distance style color #d35ed3
> distance style color #d25ed3
> distance style color #d25fd3
> distance style color #d35ed3
> distance style color #d35fd3
> distance style color #d35fd2
> distance style color #d35fcf
> distance style color #d35eca
> distance style color #d35cc3
> distance style color #d359bc
> distance style color #d356b5
> distance style color #d353ae
> distance style color #d351a8
> distance style color #d34fa4
> distance style color #d34ea1
> distance style color #d34d9f
> distance style color #d34c9e
> distance style color #d34d9d
> distance style color #d34d9c
> distance style color #d34d9a
> distance style color #d34e98
> distance style color #d34e95
> distance style color #d34e92
> distance style color #d34e90
> distance style color #d34e8d
> distance style color #d34e8b
> distance style color #d34e8a
> distance style color #d34f89
> distance style color #d34f88
> distance style color #d35087
> distance style color #d35186
> distance style color #d35285
> distance style color #d35283
> distance style color #d35382
> distance style color #d35381
> distance style color #d35380
> distance style color #d3547f
> distance style color #d3547e
> distance style color #d3547d
> distance style color #d3547b
> distance style color #d35478
> distance style color #d35476
> distance style color #d35573
> distance style color #d35571
> distance style color #d3556f
> distance style color #d3566e
> distance style color #d3566d
> distance style color #d3566c
> distance style color #d3566d
> distance style color #d3576d
> distance style color #d3566e
> distance style color #d3566f
> distance style color #d35670
> distance style color #d35771
> distance style color #d35772
> distance style color #d35873
> distance style color #d35874
> distance style color #d35875
> distance style color #d35975
> distance style color #d35976
> distance style color #d35a77
> color (#!4 & sel) #d35a77ff
> color (#!4 & sel) #d35f76ff
> color (#!4 & sel) #d36076ff
> color (#!4 & sel) #d36177ff
> color (#!4 & sel) #d36178ff
> color (#!4 & sel) #d36278ff
> color (#!4 & sel) #d36577ff
> color (#!4 & sel) #d36875ff
> color (#!4 & sel) #d36c73ff
> color (#!4 & sel) #d36f71ff
> color (#!4 & sel) #d36f70ff
> color (#!4 & sel) #d37070ff
> color (#!4 & sel) #d37071ff
> color (#!4 & sel) #d37171ff
> color (#!4 & sel) #d37672ff
> color (#!4 & sel) #d37e75ff
> color (#!4 & sel) #d38678ff
> color (#!4 & sel) #d38d7aff
> color (#!4 & sel) #d3937cff
> color (#!4 & sel) #d3967cff
> color (#!4 & sel) #d3977dff
> color (#!4 & sel) #d3967cff
> color (#!4 & sel) #d3957cff
> color (#!4 & sel) #d3937cff
> color (#!4 & sel) #d3927bff
> color (#!4 & sel) #d3917bff
> color (#!4 & sel) #d38f7aff
> color (#!4 & sel) #d38e7aff
> color (#!4 & sel) #d38d7aff
> color (#!4 & sel) #d38c7aff
> color (#!4 & sel) #d38b7aff
> color (#!4 & sel) #d38a7aff
> color (#!4 & sel) #d3897aff
> color (#!4 & sel) #d3887aff
> color (#!4 & sel) #d3877aff
> color (#!4 & sel) #d3867aff
> color (#!4 & sel) #d3857aff
> color (#!4 & sel) #d3847bff
> color (#!4 & sel) #d3827aff
> color (#!4 & sel) #d3817aff
> color (#!4 & sel) #d37e7aff
> color (#!4 & sel) #d37f7aff
> color (#!4 & sel) #d3807aff
> color (#!4 & sel) #d3847aff
> color (#!4 & sel) #d3867bff
> color (#!4 & sel) #d3877bff
> color (#!4 & sel) #d3887bff
> color (#!4 & sel) #d3897bff
> color (#!4 & sel) #d38a7cff
> color (#!4 & sel) #d38b7cff
> select #4/A:132
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/A:1-132
1033 atoms, 1052 bonds, 132 residues, 1 model selected
> color sel #d38b7cff
> select clear
> select #4/A:359
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #4/A:378
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #4/A:359
13 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 13 atom styles
> style sel stick
Changed 13 atom styles
> show sel atoms
> select clear
> select #4/A:359
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel cartoons
> select clear
> select #4/A:361
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/A:139
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select #4/A:359@N
1 atom, 1 residue, 1 model selected
> select #4/A:378@OE1
1 atom, 1 residue, 1 model selected
> select add #4/A:359@N
2 atoms, 2 residues, 1 model selected
> ui mousemode right distance
> distance #4/A:378@OE1 #4/A:359@N
Distance between fold_lptd_grand_sp_43595_hsaccharolyticum_model_0.cif #4/A
GLU 378 OE1 and GLY 359 N: 40.862Å
> hide #!5 models
> hide #!4 models
> open "/Users/vatetaud/Desktop/Protein/Deletion
> /lap1/fold_lap1x2_sp/fold_lap1x2_sp_model_0.cif"
Chain information for fold_lap1x2_sp_model_0.cif #6
---
Chain | Description
A B | .
Computing secondary structure
Drag select of 244 residues
> ui tool show "Find Cavities"
> kvfinder #6
17 cavities found for fold_lap1x2_sp_model_0.cif #6
fold_lap1x2_sp_model_0.cif Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
6.1.1 | | 221.18 | 231.18 | 1024 | 6.43 | 2.87
6.1.8 | | 47.74 | 54.97 | 221 | 1.9 | 0.54
6.1.17 | | 27.43 | 41.55 | 127 | 1.7 | 0.38
6.1.2 | | 24.41 | 51.37 | 113 | 4.02 | 1.92
6.1.11 | | 20.95 | 26.85 | 97 | 1.34 | 0.41
6.1.16 | | 20.95 | 33.49 | 97 | 2.4 | 0.83
6.1.6 | | 19.01 | 38.34 | 88 | 0 | 0
6.1.10 | | 17.5 | 38.05 | 81 | 0.6 | 0.13
6.1.7 | | 17.28 | 36.68 | 80 | 0 | 0
6.1.4 | | 16.85 | 32.3 | 78 | 0 | 0
6.1.5 | | 16.85 | 32.3 | 78 | 0 | 0
6.1.14 | | 16.85 | 32.3 | 78 | 0 | 0
6.1.9 | | 13.82 | 22.69 | 64 | 1.8 | 0.58
6.1.3 | | 8.64 | 16.79 | 40 | 1.2 | 0.34
6.1.13 | | 7.34 | 15.07 | 34 | 0.85 | 0.28
6.1.15 | | 6.48 | 10.96 | 30 | 0.85 | 0.24
6.1.12 | | 6.05 | 14.22 | 28 | 0.6 | 0.02
Populating font family aliases took 7 ms. Replace uses of missing font family
"Times" with one that exists to avoid this cost.
> color byattribute a:kvfinder_depth #6.1.1-3,8-13,15-17
1956 atoms, 12 residues, atom kvfinder_depth range 0 to 6.43
> color byattribute a:kvfinder_depth #6.1.1-3,8-13,15-17
1956 atoms, 12 residues, atom kvfinder_depth range 0 to 6.43
> view #6.1.1 @ zoom 0.75
moved plane near -31.125958660103066 [-0.85750559 -0.51428789 -0.01386201]
moved plane far -31.125958660103066 [-0.85750559 -0.51428789 -0.01386201]
> surface #6.1.1-17 transparency 50
> color #6.1.1-17 fromatoms transparency 50
> ~surface #6.1
> surface #6.1.1
> show #!6/A-B:43-45,67-69,108-113
> view #!6.1.8 @ zoom 0.75
moved plane near -15.791274704106833 [-0.22357886 0.80593182 0.5481664 ]
moved plane far -15.791274704106833 [-0.22357886 0.80593182 0.5481664 ]
> ~surface #6.1
> surface #!6.1.8
> show #!6/A:86-87,89-90/B:20,24,28,120-122
> undo
> select add #6
4092 atoms, 1752 bonds, 261 residues, 21 models selected
> select subtract #6
17 models selected
> show #!1 models
> hide #!1 models
> mlp #!6#!6.1.1-17
Map values for surface "fold_lap1x2_sp_model_0.cif_A SES surface": minimum
-28.33, mean -3.789, maximum 23.03
Map values for surface "fold_lap1x2_sp_model_0.cif_B SES surface": minimum
-28.26, mean -3.676, maximum 23.02
To also show corresponding color key, enter the above mlp command and add key
true
> hide #!6#!6.1.1-17 surfaces
> ui tool show "Find Cavities"
> kvfinder #6
17 cavities found for fold_lap1x2_sp_model_0.cif #6
fold_lap1x2_sp_model_0.cif Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
6.1.1 | | 221.18 | 231.18 | 1024 | 6.43 | 2.87
6.1.8 | | 47.74 | 54.97 | 221 | 1.9 | 0.54
6.1.17 | | 27.43 | 41.55 | 127 | 1.7 | 0.38
6.1.2 | | 24.41 | 51.37 | 113 | 4.02 | 1.92
6.1.11 | | 20.95 | 26.85 | 97 | 1.34 | 0.41
6.1.16 | | 20.95 | 33.49 | 97 | 2.4 | 0.83
6.1.6 | | 19.01 | 38.34 | 88 | 0 | 0
6.1.10 | | 17.5 | 38.05 | 81 | 0.6 | 0.13
6.1.7 | | 17.28 | 36.68 | 80 | 0 | 0
6.1.4 | | 16.85 | 32.3 | 78 | 0 | 0
6.1.5 | | 16.85 | 32.3 | 78 | 0 | 0
6.1.14 | | 16.85 | 32.3 | 78 | 0 | 0
6.1.9 | | 13.82 | 22.69 | 64 | 1.8 | 0.58
6.1.3 | | 8.64 | 16.79 | 40 | 1.2 | 0.34
6.1.13 | | 7.34 | 15.07 | 34 | 0.85 | 0.28
6.1.15 | | 6.48 | 10.96 | 30 | 0.85 | 0.24
6.1.12 | | 6.05 | 14.22 | 28 | 0.6 | 0.02
> view #6.1.1 @ zoom 0.75
moved plane near -22.604134716996935 [ 0.90306323 0.37409084 -0.21102814]
moved plane far -22.604134716996935 [ 0.90306323 0.37409084 -0.21102814]
> surface #6.1.1-17 transparency 50
> ~surface #6.1
> surface #6.1.1
> show #!6/A-B:43-45,67-69,108-113
> color byattribute a:kvfinder_depth #!6.1.1-3,8-13,15-17
1956 atoms, 12 residues, 12 surfaces, atom kvfinder_depth range 0 to 6.43
> view #!6.1.8 @ zoom 0.75
moved plane near -13.107169384330069 [ 0.9464462 0.00509193 -0.32282146]
moved plane far -13.107169384330069 [ 0.9464462 0.00509193 -0.32282146]
> ~surface #6.1
> surface #!6.1.8
> show #!6/A:86-87,89-90/B:20,24,28,120-122
> view #!6.1.1 @ zoom 0.75
moved plane near -24.177055707893413 [ 0.9464462 0.00509193 -0.32282146]
moved plane far -24.177055707893413 [ 0.9464462 0.00509193 -0.32282146]
> ~surface #6.1
> surface #!6.1.1
> show #!6/A-B:43-45,67-69,108-113
> close #6
> open "/Users/vatetaud/Desktop/Protein/Deletion
> /lap1/fold_lap1x2_sp/fold_lap1x2_sp_model_0.cif"
Chain information for fold_lap1x2_sp_model_0.cif #6
---
Chain | Description
A B | .
Computing secondary structure
> select #6
1734 atoms, 1752 bonds, 244 residues, 1 model selected
> color sel #d38b7cff
> view
> graphics silhouettes true
> lighting full
> ui mousemode right "mark surface"
> ui mousemode right "bond rotation"
> ui tool show "Find Cavities"
> ui tool show ViewDock
> ui tool show "Find Cavities"
> kvfinder #6
17 cavities found for fold_lap1x2_sp_model_0.cif #6
fold_lap1x2_sp_model_0.cif Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
6.1.1 | | 221.18 | 231.18 | 1024 | 6.43 | 2.87
6.1.8 | | 47.74 | 54.97 | 221 | 1.9 | 0.54
6.1.17 | | 27.43 | 41.55 | 127 | 1.7 | 0.38
6.1.2 | | 24.41 | 51.37 | 113 | 4.02 | 1.92
6.1.11 | | 20.95 | 26.85 | 97 | 1.34 | 0.41
6.1.16 | | 20.95 | 33.49 | 97 | 2.4 | 0.83
6.1.6 | | 19.01 | 38.34 | 88 | 0 | 0
6.1.10 | | 17.5 | 38.05 | 81 | 0.6 | 0.13
6.1.7 | | 17.28 | 36.68 | 80 | 0 | 0
6.1.4 | | 16.85 | 32.3 | 78 | 0 | 0
6.1.5 | | 16.85 | 32.3 | 78 | 0 | 0
6.1.14 | | 16.85 | 32.3 | 78 | 0 | 0
6.1.9 | | 13.82 | 22.69 | 64 | 1.8 | 0.58
6.1.3 | | 8.64 | 16.79 | 40 | 1.2 | 0.34
6.1.13 | | 7.34 | 15.07 | 34 | 0.85 | 0.28
6.1.15 | | 6.48 | 10.96 | 30 | 0.85 | 0.24
6.1.12 | | 6.05 | 14.22 | 28 | 0.6 | 0.02
> color byattribute a:kvfinder_depth #6.1.1-3,8-13,15-17
1956 atoms, 12 residues, atom kvfinder_depth range 0 to 6.43
> view #6.1.1 @ zoom 0.75
moved plane near -27.061409246234735 [0.84900576 0.17622275 0.4981313 ]
moved plane far -27.061409246234735 [0.84900576 0.17622275 0.4981313 ]
> surface #6.1.1-17 transparency 50
> color #6.1.1-17 fromatoms transparency 50
> ~surface #6.1
> surface #6.1.1
> select #!6 & (#6.1.1 @ select #6.1.1
1024 atoms, 1 residue, 1 model selected
> show #!6/A-B:43-45,67-69,108-113
> select #!6/A:108@NH2
1 atom, 1 residue, 1 model selected
> select #!6/B:108@NE
1 atom, 1 residue, 1 model selected
> select add #!6/A:108@NE
2 atoms, 2 residues, 1 model selected
Populating font family aliases took 19 ms. Replace uses of missing font family
"Times" with one that exists to avoid this cost.
> distance #!6/B:108@NE #!6/A:108@NE
Distance between fold_lap1x2_sp_model_0.cif #!6/B ARG 108 NE and /A ARG 108
NE: 17.856Å
> show #!5 models
> view #!6.1.8 @ zoom 0.75
moved plane near -12.708402947190232 [-0.97254267 -0.02950377 -0.23084693]
moved plane far -12.708402947190232 [-0.97254267 -0.02950377 -0.23084693]
> ~surface #6.1
> surface #!6.1.8
> select #!6 & (#!6.1.8 @ select #!6.1.8
221 atoms, 1 residue, 1 model selected
> show #!6/A:86-87,89-90/B:20,24,28,120-122
> view #!6.1.17 @ zoom 0.75
moved plane near -12.54223349163726 [-0.97254267 -0.02950377 -0.23084693]
moved plane far -12.54223349163726 [-0.97254267 -0.02950377 -0.23084693]
> ~surface #6.1
> surface #!6.1.17
> select #!6 & (#!6.1.17 @ select #!6.1.17
127 atoms, 1 residue, 1 model selected
> show #!6/A:20,24,28,120-122/B:86-87,89-90
> view #!6.1.8 @ zoom 0.75
moved plane near -16.484699224597843 [-0.75061338 0.09693522 -0.6535925 ]
moved plane far -16.484699224597843 [-0.75061338 0.09693522 -0.6535925 ]
> ~surface #6.1
> surface #!6.1.8
> select #!6 & (#!6.1.8 @ select #!6.1.8
221 atoms, 1 residue, 1 model selected
> show #!6/A:86-87,89-90/B:20,24,28,120-122
> view #!6.1.2 @ zoom 0.75
moved plane near -15.013868880771149 [-0.97376724 0.22747395 -0.00574465]
moved plane far -15.013868880771149 [-0.97376724 0.22747395 -0.00574465]
> ~surface #6.1
> surface #!6.1.2
> select #!6 & (#!6.1.2 @ select #!6.1.2
113 atoms, 1 residue, 1 model selected
> show #!6/A:108/B:33,36-37,41-43,47,65,67,115
> select #!6/B:114
7 atoms, 6 bonds, 1 residue, 1 model selected
> view #!6.1.17 @ zoom 0.75
moved plane near -16.946234935351 [-0.98172148 -0.18688865 -0.03599449]
moved plane far -16.946234935351 [-0.98172148 -0.18688865 -0.03599449]
> ~surface #6.1
> surface #!6.1.17
> select #!6 & (#!6.1.17 @ select #!6.1.17
127 atoms, 1 residue, 1 model selected
> show #!6/A:20,24,28,120-122/B:86-87,89-90
> view #!6.1.10 @ zoom 0.75
moved plane near -19.171909757717312 [-0.81757263 -0.39502928 -0.4189593 ]
moved plane far -19.171909757717312 [-0.81757263 -0.39502928 -0.4189593 ]
> ~surface #6.1
> surface #!6.1.10
> select #!6 & (#!6.1.10 @ select #!6.1.10
81 atoms, 1 residue, 1 model selected
> show #!6/A:117/B:52,61-63,81,93,95,117
> view #!6.1.16 @ zoom 0.75
moved plane near -14.539305096435362 [-0.88383786 0.03768197 -0.46627324]
moved plane far -14.539305096435362 [-0.88383786 0.03768197 -0.46627324]
> ~surface #6.1
> surface #!6.1.16
> select #!6 & (#!6.1.16 @ select #!6.1.16
97 atoms, 1 residue, 1 model selected
> show #!6/A:53-54,57-60,101,103
> view #!6.1.10 @ zoom 0.75
moved plane near -18.865586300966005 [-0.68486202 0.37056163 -0.62741384]
moved plane far -18.865586300966005 [-0.68486202 0.37056163 -0.62741384]
> ~surface #6.1
> surface #!6.1.10
> select #!6 & (#!6.1.10 @ select #!6.1.10
81 atoms, 1 residue, 1 model selected
> show #!6/A:117/B:52,61-63,81,93,95,117
> color #6.1.10 #c6f5b6
> color #6.1.10 #c6f5b5
> color #6.1.10 #c3f5af
> color #6.1.10 #c1f5ab
> color #6.1.10 #c0f5a9
> color #6.1.10 #b4f5a1
> color #6.1.10 #a7f597
> color #6.1.10 #a5f596
> color #6.1.10 #a3f595
> view #!6.1.11 @ zoom 0.75
moved plane near -14.547969793325057 [-0.68486202 0.37056163 -0.62741384]
moved plane far -14.547969793325057 [-0.68486202 0.37056163 -0.62741384]
> ~surface #6.1
> surface #!6.1.11
> select #!6 & (#!6.1.11 @ select #!6.1.11
97 atoms, 1 residue, 1 model selected
> show #!6/A:52,81,93,95,117/B:117
> color #6.1.10 #8ff583
> color #6.1.11 #6af59e
> color #6.1.11 #6bf59d
> color #6.1.11 #70f59c
> color #6.1.11 #7bf59b
> color #6.1.11 #82f599
> color #6.1.11 #86f598
> color #6.1.11 #8af592
> view #!6.1.4-5,7,10-11,14,16 @ zoom 0.75
moved plane near -37.804762223557084 [-0.68486202 0.37056163 -0.62741384]
moved plane far -37.804762223557084 [-0.68486202 0.37056163 -0.62741384]
> ~surface #6.1
> surface #!6.1.4-5,7,10-11,14,16
> select #!6 & (#!6.1.4-5,7,10-11,14,16 @ select #!6.1.4-5,7,10-11,14,16
589 atoms, 7 residues, 7 models selected
> show
> #!6/A:20-21,28,49,52-54,57-60,63,67,81,93,95-97,101,103,108,112-115,117-118,120/B:20-21,28,49,52,61-63,67,81,93,95-97,108,112-115,117-118,120
> view #!6.1.4-5,10-11,14,16 @ zoom 0.75
moved plane near -35.38763134015136 [-0.6514393 0.5791903 -0.4900668]
moved plane far -35.38763134015136 [-0.6514393 0.5791903 -0.4900668]
> ~surface #6.1
> surface #!6.1.4-5,10-11,14,16
> select #!6 & (#!6.1.4-5,10-11,14,16 @ select #!6.1.4-5,10-11,14,16
509 atoms, 6 residues, 6 models selected
> show
> #!6/A:20-21,28,49,52-54,57-60,63,67,81,93,95-97,101,103,108,112-115,117-118,120/B:52,61-63,67,81,93,95-97,108,112-115,117
> view #!6.1.4-5,10-11,14 @ zoom 0.75
moved plane near -32.36504218306514 [-0.6514393 0.5791903 -0.4900668]
moved plane far -32.36504218306514 [-0.6514393 0.5791903 -0.4900668]
> ~surface #6.1
> surface #!6.1.4-5,10-11,14
> select #!6 & (#!6.1.4-5,10-11,14 @ select #!6.1.4-5,10-11,14
412 atoms, 5 residues, 5 models selected
> show
> #!6/A:20-21,28,49,52,63,67,81,93,95-97,108,112-115,117-118,120/B:52,61-63,67,81,93,95-97,108,112-115,117
> view #!6.1.4-5,10-11 @ zoom 0.75
moved plane near -27.410047439647958 [-0.6514393 0.5791903 -0.4900668]
moved plane far -27.410047439647958 [-0.6514393 0.5791903 -0.4900668]
> ~surface #6.1
> surface #!6.1.4-5,10-11
> select #!6 & (#!6.1.4-5,10-11 @ select #!6.1.4-5,10-11
334 atoms, 4 residues, 4 models selected
> show
> #!6/A:52,67,81,93,95-97,108,112-115,117/B:52,61-63,67,81,93,95-97,108,112-115,117
> view #!6.1.4,10-11 @ zoom 0.75
moved plane near -26.91733395136454 [-0.6514393 0.5791903 -0.4900668]
moved plane far -26.91733395136454 [-0.6514393 0.5791903 -0.4900668]
> ~surface #6.1
> surface #!6.1.4,10-11
> select #!6 & (#!6.1.4,10-11 @ select #!6.1.4,10-11
256 atoms, 3 residues, 3 models selected
> show #!6/A:52,67,81,93,95,114-115,117/B:52,61-63,81,93,95-97,108,112-114,117
> view #!6.1.10-11 @ zoom 0.75
moved plane near -21.82197918501174 [-0.6514393 0.5791903 -0.4900668]
moved plane far -21.82197918501174 [-0.6514393 0.5791903 -0.4900668]
> ~surface #6.1
> surface #!6.1.10-11
> select #!6 & (#!6.1.10-11 @ select #!6.1.10-11
178 atoms, 2 residues, 2 models selected
> show #!6/A:52,81,93,95,117/B:52,61-63,81,93,95,117
> select #!6/B:53
8 atoms, 7 bonds, 1 residue, 1 model selected
Drag select of 16 atoms, 3 residues, 8 bonds
> select #!6/A:81@OE1
1 atom, 1 residue, 1 model selected
> select #!6/B:52@CG2
1 atom, 1 residue, 1 model selected
> select add #!6/A:81@OE1
2 atoms, 1 bond, 2 residues, 1 model selected
> select subtract #!6/A:81@OE1
1 atom, 1 residue, 1 model selected
> select add #!6/A:81@OE1
2 atoms, 2 residues, 1 model selected
> distance #!6/B:52@CG2 #!6/A:81@OE1
Distance between fold_lap1x2_sp_model_0.cif #!6/B ILE 52 CG2 and /A GLN 81
OE1: 15.435Å
> color #6.1.11 #88f5b9
> color #6.1.11 #93f5b8
> color #6.1.11 #9bf5bc
> color #6.1.11 #bff5db
> color #6.1.11 #cef5ef
> color #6.1.11 #daebf5
> color #6.1.11 #dce3f5
> color #6.1.11 #e9cff5
> color #6.1.11 #e9cef5
> color #6.1.11 #e8cef5
> color #6.1.11 #e6cdf5
> color #6.1.11 #ddc5f5
> color #6.1.11 #d1baf5
> color #6.1.11 #cfb7f5
> color #6.1.11 #ceb5f5
> color #6.1.11 #c7abf5
> color #6.1.11 #c7aaf5
> color #6.1.11 #c6aaf5
> color #6.1.11 #c3a9f5
> color #6.1.11 #c2a9f5
> color #6.1.11 #c0a9f5
> color #6.1.11 #bfa8f5
> color #6.1.11 #bea6f5
> color #6.1.11 #bca3f5
> color #6.1.11 #bba3f5
> color #6.1.11 #9b93f5
> color #6.1.11 #958ff5
> color #6.1.11 #958df5
> color #6.1.11 #9188f5
> color #6.1.11 #7f74f5
> color #6.1.11 #7e73f5
> color #6.1.11 #7b6ff5
> color #6.1.11 #7b70f5
> color #6.1.11 #7b71f5
> color #6.1.11 #7670f5
> color #6.1.11 #636cf5
> color #6.1.11 #5963f5
> color #6.1.11 #527af5
> color #6.1.11 #537ff5
> color #6.1.11 #547ff5
> color #6.1.11 #5580f5
> color #6.1.11 #567ff5
> color #6.1.11 #577ff5
> color #6.1.11 #587ff5
> color #6.1.11 #5b7ef5
> color #6.1.11 #5c7bf5
> color #6.1.11 #5c7af5
> color #6.1.10 #b2f1b4
> color #6.1.10 #b4f1b8
> color #6.1.10 #cff0f1
> color #6.1.10 #bdc7f1
> color #6.1.10 #a8a1f1
> color #6.1.10 #9f8ff1
> color #6.1.10 #9985f1
> color #6.1.10 #9882f1
> color #6.1.10 #9782f1
> color #6.1.10 #957ff1
> color #6.1.10 #9177f1
> color #6.1.10 #8d77f1
> color #6.1.10 #8b7df1
> color #6.1.10 #8b82f1
> color #6.1.10 #8a86f1
> color #6.1.10 #8a88f1
> color #6.1.10 #8a89f1
> color #6.1.10 #8c8ff1
> color #6.1.10 #939df1
> color #6.1.10 #95a1f1
> color #6.1.10 #9babf1
> color #6.1.10 #a1bcf1
> color #6.1.10 #a1bdf1
> color #6.1.10 #a0baf1
> color #6.1.10 #9eb8f1
> color #6.1.10 #96b5f1
> color #6.1.10 #95b5f1
> color #6.1.10 #91c8f1
> color #6.1.10 #90c8f1
> color #6.1.10 #88bdf1
> color #6.1.10 #7eb4f1
> color #6.1.10 #77abf1
> color #6.1.10 #76aaf1
> color #6.1.10 #74b9f1
> color #6.1.10 #73bef1
> color #6.1.10 #74b8f1
> color #6.1.10 #73a0f1
> color #6.1.10 #7399f1
> color #6.1.10 #7497f1
> color #6.1.10 #7590f1
> color #6.1.10 #758df1
> color #6.1.10 #768cf1
> color #6.1.10 #778cf1
> color #6.1.10 #7989f1
> color #6.1.10 #7988f1
> color #6.1.10 #7a8af1
> color #6.1.10 #7f91f1
> color #6.1.10 #8093f1
> color #6.1.10 #8194f1
> color #6.1.10 #849af1
> color #6.1.10 #89a3f1
> color #6.1.10 #8aa8f1
> color #6.1.10 #8ba9f1
> color #6.1.10 #8cacf1
> color #6.1.10 #8eb1f1
> color #6.1.10 #8faef1
> color #6.1.10 #8fabf1
> color #6.1.10 #90a5f1
> color #6.1.10 #8d9ef1
> color #6.1.10 #8895f1
> color #6.1.10 #838cf1
> color #6.1.10 #817ff1
> color #6.1.10 #807ef1
> color #6.1.10 #7e7df1
> color #6.1.10 #7c7df1
> color #6.1.10 #797ef1
> color #6.1.10 #7988f1
> color #6.1.10 #798df1
> color #6.1.10 #7a90f1
> color #6.1.10 #7b91f1
> color #6.1.10 #7c90f1
> color #6.1.10 #7e90f1
> color #6.1.10 #7f91f1
> color #6.1.10 #7f93f1
> color #6.1.10 #8094f1
> color #6.1.10 #8197f1
> color #6.1.10 #829cf1
> color #6.1.10 #819bf1
> color #6.1.10 #829af1
> color #6.1.10 #8299f1
> color #6.1.10 #8296f1
> color #6.1.10 #8394f1
> color #6.1.10 #8493f1
> color #6.1.10 #8492f1
> color #6.1.10 #8491f1
> view #!6.1.1 @ zoom 0.75
moved plane near -23.72298270621744 [ 0.49951015 -0.11965271 0.85800516]
moved plane far -23.72298270621744 [ 0.49951015 -0.11965271 0.85800516]
> ~surface #6.1
> surface #!6.1.1
> select #!6 & (#!6.1.1 @ select #!6.1.1
1024 atoms, 1 residue, 1 model selected
> show #!6/A-B:43-45,67-69,108-113
> mlp sel
mlp: no amino acids specified
> mlp sel
mlp: no amino acids specified
> view #!6.1.16 @ zoom 0.75
moved plane near -16.011671135320736 [-0.96200577 0.18018354 -0.20513124]
moved plane far -16.011671135320736 [-0.96200577 0.18018354 -0.20513124]
> ~surface #6.1
> surface #!6.1.16
> select #!6 & (#!6.1.16 @ select #!6.1.16
97 atoms, 1 residue, 1 model selected
> show #!6/A:53-54,57-60,101,103
> view #!6.1.10 @ zoom 0.75
moved plane near -20.180647625910392 [-0.96200577 0.18018354 -0.20513124]
moved plane far -20.180647625910392 [-0.96200577 0.18018354 -0.20513124]
> ~surface #6.1
> surface #!6.1.10
> select #!6 & (#!6.1.10 @ select #!6.1.10
81 atoms, 1 residue, 1 model selected
> show #!6/A:117/B:52,61-63,81,93,95,117
> view #!6.1.11 @ zoom 0.75
moved plane near -17.11213269306369 [-0.96200577 0.18018354 -0.20513124]
moved plane far -17.11213269306369 [-0.96200577 0.18018354 -0.20513124]
> ~surface #6.1
> surface #!6.1.11
> select #!6 & (#!6.1.11 @ select #!6.1.11
97 atoms, 1 residue, 1 model selected
> show #!6/A:52,81,93,95,117/B:117
> view #!6.1.10-11 @ zoom 0.75
moved plane near -25.187514522114487 [-0.96200577 0.18018354 -0.20513124]
moved plane far -25.187514522114487 [-0.96200577 0.18018354 -0.20513124]
> ~surface #6.1
> surface #!6.1.10-11
> select #!6 & (#!6.1.10-11 @ select #!6.1.10-11
178 atoms, 2 residues, 2 models selected
> show #!6/A:52,81,93,95,117/B:52,61-63,81,93,95,117
> mlp sel
mlp: no amino acids specified
> mlp sel
mlp: no amino acids specified
> mlp sel
mlp: no amino acids specified
> view #!6.1.1 @ zoom 0.75
moved plane near -27.33729251885039 [-0.96200577 0.18018354 -0.20513124]
moved plane far -27.33729251885039 [-0.96200577 0.18018354 -0.20513124]
> ~surface #6.1
> surface #!6.1.1
> select #!6 & (#!6.1.1 @ select #!6.1.1
1024 atoms, 1 residue, 1 model selected
> show #!6/A-B:43-45,67-69,108-113
> select #6
4092 atoms, 1752 bonds, 2 pseudobonds, 261 residues, 20 models selected
> mlp sel
Map values for surface "fold_lap1x2_sp_model_0.cif_A SES surface": minimum
-28.33, mean -3.789, maximum 23.03
Map values for surface "fold_lap1x2_sp_model_0.cif_B SES surface": minimum
-28.26, mean -3.676, maximum 23.02
To also show corresponding color key, enter the above mlp command and add key
true
> view
> hide #!5 models
> close #10
> close #6
> open "/Users/vatetaud/Desktop/Protein/Deletion
> /Lap2/fold_lap2_sp/fold_lap2_sp_model_0.cif"
Chain information for fold_lap2_sp_model_0.cif #6
---
Chain | Description
A | .
Computing secondary structure
> select #6
2579 atoms, 2606 bonds, 351 residues, 1 model selected
> color sel medium blue
> ui tool show "Find Cavities"
> kvfinder #6
12 cavities found for fold_lap2_sp_model_0.cif #6
fold_lap2_sp_model_0.cif Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
6.1.11 | | 283.61 | 276.99 | 1313 | 3.84 | 1.03
6.1.6 | | 110.16 | 129.26 | 510 | 3.39 | 0.84
6.1.2 | | 77.76 | 99.51 | 360 | 3.29 | 1.45
6.1.10 | | 66.96 | 85.65 | 310 | 2.68 | 0.77
6.1.12 | | 57.89 | 90.17 | 268 | 0 | 0
6.1.4 | | 43.42 | 69.87 | 201 | 0 | 0
6.1.1 | | 38.02 | 44.71 | 176 | 1.7 | 0.5
6.1.3 | | 33.05 | 42.59 | 153 | 1.47 | 0.43
6.1.9 | | 25.49 | 40.78 | 118 | 0 | 0
6.1.7 | | 17.93 | 27.97 | 83 | 1.34 | 0.5
6.1.8 | | 15.77 | 29.32 | 73 | 1.2 | 0.38
6.1.5 | | 11.45 | 24.03 | 53 | 1.2 | 0.23
> color byattribute a:kvfinder_depth #6.1.1-3,5-8,10-11
3031 atoms, 9 residues, atom kvfinder_depth range 0 to 3.84
> ui tool show "Find Cavities"
> kvfinder #6
12 cavities found for fold_lap2_sp_model_0.cif #6
fold_lap2_sp_model_0.cif Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
6.1.11 | | 283.61 | 276.99 | 1313 | 3.84 | 1.03
6.1.6 | | 110.16 | 129.26 | 510 | 3.39 | 0.84
6.1.2 | | 77.76 | 99.51 | 360 | 3.29 | 1.45
6.1.10 | | 66.96 | 85.65 | 310 | 2.68 | 0.77
6.1.12 | | 57.89 | 90.17 | 268 | 0 | 0
6.1.4 | | 43.42 | 69.87 | 201 | 0 | 0
6.1.1 | | 38.02 | 44.71 | 176 | 1.7 | 0.5
6.1.3 | | 33.05 | 42.59 | 153 | 1.47 | 0.43
6.1.9 | | 25.49 | 40.78 | 118 | 0 | 0
6.1.7 | | 17.93 | 27.97 | 83 | 1.34 | 0.5
6.1.8 | | 15.77 | 29.32 | 73 | 1.2 | 0.38
6.1.5 | | 11.45 | 24.03 | 53 | 1.2 | 0.23
> color byattribute a:kvfinder_depth #6.1.1-3,5-8,10-11
3031 atoms, 9 residues, atom kvfinder_depth range 0 to 3.84
> view #6.1.11 @ zoom 0.75
moved plane near -27.71425943727883 [-0.83940726 -0.44868236 -0.306724 ]
moved plane far -27.71425943727883 [-0.83940726 -0.44868236 -0.306724 ]
> surface #6.1.1-12 transparency 50
> color #6.1.1-12 fromatoms transparency 50
> ~surface #6.1
> surface #6.1.11
> select #!6 & (#6.1.11 @ select #6.1.11
1313 atoms, 1 residue, 1 model selected
> show #!6/A:195-199,224,227-228,231,235-247,256-262
Populating font family aliases took 10 ms. Replace uses of missing font family
"Times" with one that exists to avoid this cost.
> mlp sel
mlp: no amino acids specified
> select #6
6197 atoms, 2606 bonds, 363 residues, 14 models selected
> mlp sel
Map values for surface "fold_lap2_sp_model_0.cif_A SES surface": minimum
-28.04, mean -6.596, maximum 22.28
To also show corresponding color key, enter the above mlp command and add key
true
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/vatetaud/Desktop/movie3.mp4
Movie saved to /Users/vatetaud/Desktop/movie3.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/vatetaud/Desktop/movie4.mp4
Movie saved to /Users/vatetaud/Desktop/movie4.mp4
> hide sel surfaces
> view #!6.1.6 @ zoom 0.75
moved plane near -20.842152079924887 [-0.46155622 0.78009523 -0.42239472]
moved plane far -20.842152079924887 [-0.46155622 0.78009523 -0.42239472]
> ~surface #6.1
> surface #!6.1.6
> select #!6 & (#!6.1.6 @ select #!6.1.6
510 atoms, 1 residue, 1 model selected
> show #!6/A:12,57,61,70,74,84-87,92,175-176,178-180,208-212,214
> view
> view #!6.1.6,11 @ zoom 0.75
moved plane near -56.705825757454456 [-0.27091912 -0.31354876 -0.9101044 ]
moved plane far -56.705825757454456 [-0.27091912 -0.31354876 -0.9101044 ]
> ~surface #6.1
> surface #!6.1.6,11
> select #!6 & (#!6.1.6,11 @ select #!6.1.6,11
1823 atoms, 2 residues, 2 models selected
> show
> #!6/A:12,57,61,70,74,84-87,92,175-176,178-180,195-199,208-212,214,224,227-228,231,235-247,256-262
> view
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/vatetaud/Desktop/movie5.mp4
Movie saved to /Users/vatetaud/Desktop/movie5.mp4
> save "/Users/vatetaud/Desktop/Protein/Deletion
> /Lap2/fold_lap2_sp/fold_lap2_sp_cavity.cxs"
> open "/Users/vatetaud/Desktop/Protein/Deletion
> /lap1/fold_lap1x2_sp/fold_lap1x2_sp_model_0.cif"
Chain information for fold_lap1x2_sp_model_0.cif #7
---
Chain | Description
A B | .
Computing secondary structure
> close #6
> ui tool show "Find Cavities"
> kvfinder #7
17 cavities found for fold_lap1x2_sp_model_0.cif #7
fold_lap1x2_sp_model_0.cif Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
7.1.1 | | 221.18 | 231.18 | 1024 | 6.43 | 2.87
7.1.8 | | 47.74 | 54.97 | 221 | 1.9 | 0.54
7.1.17 | | 27.43 | 41.55 | 127 | 1.7 | 0.38
7.1.2 | | 24.41 | 51.37 | 113 | 4.02 | 1.92
7.1.11 | | 20.95 | 26.85 | 97 | 1.34 | 0.41
7.1.16 | | 20.95 | 33.49 | 97 | 2.4 | 0.83
7.1.6 | | 19.01 | 38.34 | 88 | 0 | 0
7.1.10 | | 17.5 | 38.05 | 81 | 0.6 | 0.13
7.1.7 | | 17.28 | 36.68 | 80 | 0 | 0
7.1.4 | | 16.85 | 32.3 | 78 | 0 | 0
7.1.5 | | 16.85 | 32.3 | 78 | 0 | 0
7.1.14 | | 16.85 | 32.3 | 78 | 0 | 0
7.1.9 | | 13.82 | 22.69 | 64 | 1.8 | 0.58
7.1.3 | | 8.64 | 16.79 | 40 | 1.2 | 0.34
7.1.13 | | 7.34 | 15.07 | 34 | 0.85 | 0.28
7.1.15 | | 6.48 | 10.96 | 30 | 0.85 | 0.24
7.1.12 | | 6.05 | 14.22 | 28 | 0.6 | 0.02
> color byattribute a:kvfinder_depth #7.1.1-3,8-13,15-17
1956 atoms, 12 residues, atom kvfinder_depth range 0 to 6.43
> view #7.1.1 @ zoom 0.75
moved plane near -24.761416809315786 [-0.0075937 0.92096027 -0.38958252]
moved plane far -24.761416809315786 [-0.0075937 0.92096027 -0.38958252]
> surface #7.1.1-17 transparency 50
> color #7.1.1-17 fromatoms transparency 50
> ~surface #7.1
> surface #7.1.1
> select #!7 & (#7.1.1 @ select #7.1.1
1024 atoms, 1 residue, 1 model selected
> show #!7/A-B:43-45,67-69,108-113
> view #!7.1.9 @ zoom 0.75
moved plane near -12.070348786215753 [-0.01108152 0.88612304 -0.46331758]
moved plane far -12.070348786215753 [-0.01108152 0.88612304 -0.46331758]
> ~surface #7.1
> surface #!7.1.9
> select #!7 & (#!7.1.9 @ select #!7.1.9
64 atoms, 1 residue, 1 model selected
> show #!7/A:55,80,98,103,106-107/B:41
> view #!7.1.3 @ zoom 0.75
moved plane near -11.208285647160835 [-0.01108152 0.88612304 -0.46331758]
moved plane far -11.208285647160835 [-0.01108152 0.88612304 -0.46331758]
> ~surface #7.1
> surface #!7.1.3
> select #!7 & (#!7.1.3 @ select #!7.1.3
40 atoms, 1 residue, 1 model selected
> show #!7/A:41/B:55,80,98,103,106-107
> view #!7.1.13 @ zoom 0.75
moved plane near -11.86948019332055 [-0.01108152 0.88612304 -0.46331758]
moved plane far -11.86948019332055 [-0.01108152 0.88612304 -0.46331758]
> ~surface #7.1
> surface #!7.1.13
> select #!7 & (#!7.1.13 @ select #!7.1.13
34 atoms, 1 residue, 1 model selected
> show #!7/A:85,87-91/B:121
> view #!7.1.15 @ zoom 0.75
moved plane near -12.811544072106082 [-0.01108152 0.88612304 -0.46331758]
moved plane far -12.811544072106082 [-0.01108152 0.88612304 -0.46331758]
> ~surface #7.1
> surface #!7.1.15
> select #!7 & (#!7.1.15 @ select #!7.1.15
30 atoms, 1 residue, 1 model selected
> show #!7/A:17-18,21-22,51,60
> view #!7.1.12 @ zoom 0.75
moved plane near -14.04005115068538 [-0.01108152 0.88612304 -0.46331758]
moved plane far -14.04005115068538 [-0.01108152 0.88612304 -0.46331758]
> ~surface #7.1
> surface #!7.1.12
> select #!7 & (#!7.1.12 @ select #!7.1.12
28 atoms, 1 residue, 1 model selected
> show #!7/B:13,16-17,120,122
> view #!7.1.10 @ zoom 0.75
moved plane near -16.502304700748184 [-0.01108152 0.88612304 -0.46331758]
moved plane far -16.502304700748184 [-0.01108152 0.88612304 -0.46331758]
> ~surface #7.1
> surface #!7.1.10
> select #!7 & (#!7.1.10 @ select #!7.1.10
81 atoms, 1 residue, 1 model selected
> show #!7/A:117/B:52,61-63,81,93,95,117
> view #!7.1.5 @ zoom 0.75
moved plane near -14.865165761270987 [-0.54731525 0.06725025 -0.83422026]
moved plane far -14.865165761270987 [-0.54731525 0.06725025 -0.83422026]
> ~surface #7.1
> surface #!7.1.5
> select #!7 & (#!7.1.5 @ select #!7.1.5
78 atoms, 1 residue, 1 model selected
> show #!7/A:95-97,108,112-114/B:67,114-115
> view #!7.1.10 @ zoom 0.75
moved plane near -18.960531008187672 [-0.54731525 0.06725025 -0.83422026]
moved plane far -18.960531008187672 [-0.54731525 0.06725025 -0.83422026]
> ~surface #7.1
> surface #!7.1.10
> select #!7 & (#!7.1.10 @ select #!7.1.10
81 atoms, 1 residue, 1 model selected
> show #!7/A:117/B:52,61-63,81,93,95,117
> view #!7.1.9 @ zoom 0.75
moved plane near -15.443774410483902 [-0.35703425 -0.2843109 -0.88977181]
moved plane far -15.443774410483902 [-0.35703425 -0.2843109 -0.88977181]
> ~surface #7.1
> surface #!7.1.9
> select #!7 & (#!7.1.9 @ select #!7.1.9
64 atoms, 1 residue, 1 model selected
> show #!7/A:55,80,98,103,106-107/B:41
> view #!7.1.4 @ zoom 0.75
moved plane near -15.771343658739555 [-0.6258038 -0.40665492 -0.66558351]
moved plane far -15.771343658739555 [-0.6258038 -0.40665492 -0.66558351]
> ~surface #7.1
> surface #!7.1.4
> select #!7 & (#!7.1.4 @ select #!7.1.4
78 atoms, 1 residue, 1 model selected
> show #!7/A:67,114-115/B:95-97,108,112-114
> view #!7.1.3 @ zoom 0.75
moved plane near -14.32925308289731 [-0.6258038 -0.40665492 -0.66558351]
moved plane far -14.32925308289731 [-0.6258038 -0.40665492 -0.66558351]
> ~surface #7.1
> surface #!7.1.3
> select #!7 & (#!7.1.3 @ select #!7.1.3
40 atoms, 1 residue, 1 model selected
> show #!7/A:41/B:55,80,98,103,106-107
> view #!7.1.13 @ zoom 0.75
moved plane near -14.157257716450507 [-0.6258038 -0.40665492 -0.66558351]
moved plane far -14.157257716450507 [-0.6258038 -0.40665492 -0.66558351]
> ~surface #7.1
> surface #!7.1.13
> select #!7 & (#!7.1.13 @ select #!7.1.13
34 atoms, 1 residue, 1 model selected
> show #!7/A:85,87-91/B:121
> view #!7.1.5 @ zoom 0.75
moved plane near -15.17863281739283 [-0.6258038 -0.40665492 -0.66558351]
moved plane far -15.17863281739283 [-0.6258038 -0.40665492 -0.66558351]
> ~surface #7.1
> surface #!7.1.5
> select #!7 & (#!7.1.5 @ select #!7.1.5
78 atoms, 1 residue, 1 model selected
> show #!7/A:95-97,108,112-114/B:67,114-115
> view #!7.1.14 @ zoom 0.75
moved plane near -11.06245230975077 [-0.6258038 -0.40665492 -0.66558351]
moved plane far -11.06245230975077 [-0.6258038 -0.40665492 -0.66558351]
> ~surface #7.1
> surface #!7.1.14
> select #!7 & (#!7.1.14 @ select #!7.1.14
78 atoms, 1 residue, 1 model selected
> show #!7/A:20-21,28,49,63,118,120
> view #!7.1.7 @ zoom 0.75
moved plane near -13.137150701372148 [-0.6258038 -0.40665492 -0.66558351]
moved plane far -13.137150701372148 [-0.6258038 -0.40665492 -0.66558351]
> ~surface #7.1
> surface #!7.1.7
> select #!7 & (#!7.1.7 @ select #!7.1.7
80 atoms, 1 residue, 1 model selected
> show #!7/B:20-21,28,49,63,118,120
> view #!7.1.10 @ zoom 0.75
moved plane near -18.768455649065714 [-0.6258038 -0.40665492 -0.66558351]
moved plane far -18.768455649065714 [-0.6258038 -0.40665492 -0.66558351]
> ~surface #7.1
> surface #!7.1.10
> select #!7 & (#!7.1.10 @ select #!7.1.10
81 atoms, 1 residue, 1 model selected
> show #!7/A:117/B:52,61-63,81,93,95,117
> view #!7.1.11 @ zoom 0.75
moved plane near -14.877634976073429 [-0.6258038 -0.40665492 -0.66558351]
moved plane far -14.877634976073429 [-0.6258038 -0.40665492 -0.66558351]
> ~surface #7.1
> surface #!7.1.11
> select #!7 & (#!7.1.11 @ select #!7.1.11
97 atoms, 1 residue, 1 model selected
> show #!7/A:52,81,93,95,117/B:117
> view #!7.1.6,10-11 @ zoom 0.75
moved plane near -27.641652114120756 [-0.67579906 -0.37858377 -0.6324318 ]
moved plane far -27.641652114120756 [-0.67579906 -0.37858377 -0.6324318 ]
> ~surface #7.1
> surface #!7.1.6,10-11
> select #!7 & (#!7.1.6,10-11 @ select #!7.1.6,10-11
266 atoms, 3 residues, 3 models selected
> show #!7/A:33,36,43,47,52,65,81,93,95,115,117/B:52,61-63,81,93,95,108,117
> view #!7.1.10-11 @ zoom 0.75
moved plane near -22.019034983401387 [-0.67579906 -0.37858377 -0.6324318 ]
moved plane far -22.019034983401387 [-0.67579906 -0.37858377 -0.6324318 ]
> ~surface #7.1
> surface #!7.1.10-11
> select #!7 & (#!7.1.10-11 @ select #!7.1.10-11
178 atoms, 2 residues, 2 models selected
> show #!7/A:52,81,93,95,117/B:52,61-63,81,93,95,117
> view #!7.1.1,10-11 @ zoom 0.75
moved plane near -32.68024535019525 [-0.67579906 -0.37858377 -0.6324318 ]
moved plane far -32.68024535019525 [-0.67579906 -0.37858377 -0.6324318 ]
> ~surface #7.1
> surface #!7.1.1,10-11
> select #!7 & (#!7.1.1,10-11 @ select #!7.1.1,10-11
1202 atoms, 3 residues, 3 models selected
> show
> #!7/A:43-45,52,67-69,81,93,95,108-113,117/B:43-45,52,61-63,67-69,81,93,95,108-113,117
> view
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/vatetaud/Desktop/movie6.mp4
Movie saved to /Users/vatetaud/Desktop/movie6.mp4
> mlp sel
mlp: no amino acids specified
> mlp sel
mlp: no amino acids specified
> select #7
4092 atoms, 1752 bonds, 261 residues, 19 models selected
> mlp sel
Map values for surface "fold_lap1x2_sp_model_0.cif_A SES surface": minimum
-28.33, mean -3.789, maximum 23.03
Map values for surface "fold_lap1x2_sp_model_0.cif_B SES surface": minimum
-28.26, mean -3.676, maximum 23.02
To also show corresponding color key, enter the above mlp command and add key
true
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/vatetaud/Desktop/movie7.mp4
Movie saved to /Users/vatetaud/Desktop/movie7.mp4
> select #7
4092 atoms, 1752 bonds, 261 residues, 19 models selected
> close #7
> open "/Users/vatetaud/Desktop/Protein/Deletion
> /RuvC/Initial/fold_ruvc_omc_vp/fold_ruvc_omc_vp_model_0.cif"
Chain information for fold_ruvc_omc_vp_model_0.cif #6
---
Chain | Description
A | .
Computing secondary structure
> select #6
1394 atoms, 1423 bonds, 175 residues, 1 model selected
> color sel blue
> color sel #7aec7dff
> color sel #7bec7dff
> color sel #7bec7eff
> color sel #7dec80ff
> color sel #83ec89ff
> color sel #8fec9cff
> color sel #9becb0ff
> color sel #a6ecc5ff
> color sel #afecdaff
> color sel #b1e9ecff
> color sel #add6ecff
> color sel #a7c7ecff
> color sel #a1bbecff
> color sel #9cb2ecff
> color sel #98acecff
> color sel #96a9ecff
> color sel #94a5ecff
> color sel #93a3ecff
> color sel #91a0ecff
> color sel #8f9cecff
> color sel #8c98ecff
> color sel #8a94ecff
> color sel #888eecff
> color sel #8588ecff
> color sel #8385ecff
> color sel #8282ecff
> color sel #8382ecff
> color sel #8483ecff
> color sel #8684ecff
> color sel #8886ecff
> color sel #8b88ecff
> color sel #8f8aecff
> color sel #938cecff
> color sel #968eecff
> color sel #988fecff
> color sel #9a91ecff
> color sel #9d94ecff
> color sel #a197ecff
> color sel #a59aecff
> color sel #a99cecff
> color sel #ad9fecff
> color sel #b0a1ecff
> color sel #b3a4ecff
> color sel #b5a6ecff
> color sel #b8a8ecff
> color sel #baaaecff
> color sel #bbabecff
> color sel #bcabecff
> color sel #bbabecff
> color sel #baabecff
> color sel #b9aaecff
> color sel #b8aaecff
> color sel #b8a9ecff
> color sel #b7a8ecff
> color sel #b6a7ecff
> color sel #b5a6ecff
> color sel #b3a5ecff
> color sel #b2a4ecff
> color sel #b1a4ecff
> color sel #b0a3ecff
> color sel #afa3ecff
> color sel #aea2ecff
> color sel #aca1ecff
> color sel #aba0ecff
> color sel #aaa0ecff
> color sel #aa9fecff
> color sel #a99fecff
> color sel #a89eecff
> color sel #a79decff
> color sel #a59cecff
> color sel #a39aecff
> color sel #a098ecff
> color sel #9c95ecff
> color sel #9791ecff
> color sel #938eecff
> color sel #908cecff
> color sel #8d8aecff
> color sel #8b88ecff
> color sel #8887ecff
> color sel #8785ecff
> color sel #8584ecff
> color sel #8484ecff
> color sel #8383ecff
> color sel #8183ecff
> color sel #7f83ecff
> color sel #7e83ecff
> color sel #7d83ecff
> color sel #7d84ecff
> color sel #7d85ecff
> color sel #7e85ecff
> color sel #7e86ecff
> color sel #7f87ecff
> color sel #8088ecff
> color sel #8089ecff
> color sel #8189ecff
> color sel #8289ecff
> color sel #8389ecff
> color sel #848aecff
> color sel #858aecff
> color sel #868aecff
> color sel #878becff
> color sel #878cecff
> color sel #888decff
> color sel #898eecff
> color sel #8a8fecff
> color sel #8a90ecff
> color sel #8b91ecff
> color sel #8b92ecff
> color sel #8c93ecff
> color sel #8d94ecff
> color sel #8d95ecff
> color sel #8c96ecff
> color sel #8c97ecff
> color sel #8b98ecff
> color sel #8a98ecff
> color sel #8a99ecff
> color sel #8a9aecff
> color sel #899aecff
> color sel #8a9becff
> color sel #8a9cecff
> color sel #8b9decff
> color sel #8c9decff
> color sel #8c9eecff
> color sel #8ea0ecff
> color sel #90a2ecff
> color sel #91a3ecff
> color sel #93a5ecff
> color sel #94a5ecff
> color sel #95a6ecff
> color sel #94a5ecff
> color sel #94a4ecff
> color sel #93a3ecff
> color sel #92a1ecff
> color sel #919fecff
> color sel #909decff
> color sel #8f9cecff
> color sel #8e9aecff
> color sel #8d99ecff
> color sel #8c98ecff
> color sel #8c96ecff
> color sel #8b95ecff
> color sel #8a95ecff
> color sel #8993ecff
> color sel #8892ecff
> color sel #8791ecff
> color sel #8691ecff
> select clear
> ui tool show "Find Cavities"
> kvfinder #6
2 cavities found for fold_ruvc_omc_vp_model_0.cif #6
fold_ruvc_omc_vp_model_0.cif Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
6.1.2 | | 30.67 | 50.76 | 142 | 3 | 1.54
6.1.1 | | 19.87 | 25.09 | 92 | 1.34 | 0.32
> color byattribute a:kvfinder_depth #6.1.1-2
234 atoms, 2 residues, atom kvfinder_depth range 0 to 3
> close #6
> open "/Users/vatetaud/Desktop/Protein/Deletion
> /LpxA/alignement_LpxA_Ec_LpxA_VP/4d45f96aa4adc4a6.A.cif"
Chain information for 4d45f96aa4adc4a6.A.cif #6
---
Chain | Description
A | .
Computing secondary structure
> close #6
> open /Users/vatetaud/Desktop/Protein/TIM/Bam/Bam_complex_E.coli.cif
Summary of feedback from opening
/Users/vatetaud/Desktop/Protein/TIM/Bam/Bam_complex_E.coli.cif
---
warnings | Atom H is not in the residue template for LEU /B:22
Atom H is not in the residue template for CYS /C:25
Atom H is not in the residue template for GLU /D:26
Atom H is not in the residue template for GLU /E:24
Atom H is not in the residue template for PHE /A:24
Bam_complex_E.coli.cif title:
E. coli BAM complex (BamABCDE) by cryoEM [more info...]
Chain information for Bam_complex_E.coli.cif #6
---
Chain | Description | UniProt
A | Outer membrane protein assembly factor BamA | BAMA_ECO45 24-806
B | Outer membrane protein assembly factor BamB | BAMB_ECOLI 22-392
C | Outer membrane protein assembly factor BamC | BAMC_ECOLI 25-189
D | Outer membrane protein assembly factor BamD | BAMD_ECO57 26-243
E | Outer membrane protein assembly factor BamE | BAME_ECOL6 24-110
> view
> hide #6 surfaces
> select #6
24947 atoms, 25220 bonds, 1624 residues, 1 model selected
> hide sel surfaces
> show sel cartoons
> hide sel atoms
> select clear
> show #6 surfaces
> save /Users/vatetaud/Desktop/image12.png supersample 3
> open
> /Users/vatetaud/Desktop/Protein/OM_biogenesis/BamA_Vp/fold_bama_model_0.cif
Chain information for fold_bama_model_0.cif #7
---
Chain | Description
A | .
Computing secondary structure
> hide #5.1 models
> show #5.1 models
> hide #5.1 models
> hide #!5 models
> hide #!6 models
> view
> show #7 surfaces
> show #!6 models
> select #7
5404 atoms, 5515 bonds, 695 residues, 1 model selected
> color (#!7 & sel) #ffff9dff
> color (#!7 & sel) #b4bf6cff
> color (#!7 & sel) #f8fd96ff
> hide #!6 models
> select clear
> save /Users/vatetaud/Desktop/image13.png supersample 3
> hide #!7 surfaces
> select #7/A:353
9 atoms, 8 bonds, 1 residue, 1 model selected
===== 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.
How to cite UCSF ChimeraX
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: Z1KK000ABFN/A
Chip: Apple M5
Total Number of Cores: 10 (4 Super and 6 Efficiency)
Memory: 24 GB
System Firmware Version: 18000.101.7
OS Loader Version: 18000.101.7
Software:
System Software Overview:
System Version: macOS 26.4.1 (25E253)
Kernel Version: Darwin 25.4.0
Time since boot: 21 jours, 13 heures et 50 minutes
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 P2719H:
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-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-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-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
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
narwhals: 2.21.2
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: 2.4.6
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 25.0
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
plotly: 6.7.0
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
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
pyKVFinder: 0.9.2
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
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
tomlkit: 0.15.0
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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