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Opened 9 months ago
Closed 9 months ago
#16723 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.2-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x00000001f6ad4100 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, chimerax.pdb_lib._load_libs, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, psutil._psutil_osx, psutil._psutil_posix, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, lxml._elementpath, lxml.etree (total: 121)
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"incident" : "09C50983-E8D6-46B0-9696-815AD838FA43",
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"procLaunch" : "2025-01-27 09:09:51.0293 +0100",
"procStartAbsTime" : 8530472668353,
"procExitAbsTime" : 9558140439543,
"procName" : "ChimeraX",
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"ktriageinfo" : "VM - pmap_enter retried due to resource shortage\n",
"vmregioninfo" : "0x64af6989f028 is not in any region. Bytes after previous region: 5149288951849 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO (reserved) 600078000000-600080000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)\n---> \n UNUSED SPACE AT END",
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.7G resident=0K(0%) swapped_out_or_unallocated=1.7G(100%)\nWritable regions: Total=5.6G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=5.6G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG backing stores 2944K 8 \nCG image 3200K 138 \nCG raster data 384K 8 \nColorSync 592K 29 \nCoreAnimation 2960K 150 \nCoreGraphics 128K 8 \nCoreServices 624K 2 \nCoreUI image data 6016K 49 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 3.6G 1624 \nMALLOC guard page 192K 9 \nMALLOC_MEDIUM (reserved) 520.0M 6 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)\nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 720K 45 \nStack 196.5M 46 \nStack Guard 56.0M 1 \nVM_ALLOCATE 568.8M 636 \nVM_ALLOCATE (reserved) 352.0M 4 reserved VM address space (unallocated)\n__AUTH 2019K 391 \n__AUTH_CONST 25.5M 624 \n__CTF 756 1 \n__DATA 23.2M 851 \n__DATA_CONST 40.5M 848 \n__DATA_DIRTY 2050K 248 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__LINKEDIT 804.8M 223 \n__OBJC_CONST 5005K 358 \n__OBJC_RO 65.5M 1 \n__OBJC_RW 1988K 1 \n__TEXT 901.4M 869 \ndyld private memory 560K 6 \nmapped file 555.2M 82 \nshared memory 3184K 26 \n=========== ======= ======= \nTOTAL 8.0G 7309 \nTOTAL, minus reserved VM space 6.8G 7309 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "6297d96be2c9387df974efa4",
"factorPackIds" : {
},
"deploymentId" : 240000032
},
{
"rolloutId" : "6112d17137f5d11121dcd4e2",
"factorPackIds" : {
},
"deploymentId" : 240000570
}
],
"experiments" : [
]
},
"reportNotes" : [
"dyld_process_snapshot_create_for_process failed with 5"
]
}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/nezakoritnik/Desktop/HCPro-struktura/monomerhcpro.cif
Summary of feedback from opening /Users/nezakoritnik/Desktop/HCPro-
struktura/monomerhcpro.cif
---
warnings | Unknown polymer entity '1' on line 131
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for monomerhcpro.cif #1
---
Chain | Description
Ab | No description available
> set bgColor white
> open "/Users/nezakoritnik/Documents/REZULTATI/Bioinformatske
> analize/AlphaFold/ALFAFOLD3/PVA-
> HCPro_2024_05_09_pva_hcpro/fold_2024_05_09_pva_hcpro_model_0.cif"
Chain information for fold_2024_05_09_pva_hcpro_model_0.cif #2
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #2 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 monomerhcpro.cif, chain Ab (#1) with
fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score
= 1127.3
RMSD between 151 pruned atom pairs is 0.771 angstroms; (across all 261 pairs:
36.016)
> ui tool show Matchmaker
> ui tool show "Show Sequence Viewer"
> sequence chain #1/Ab
Alignment identifier is 1/Ab
> select #1/Ab:102
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/Ab:102-174
584 atoms, 594 bonds, 73 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #2 to #1 & sel
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 monomerhcpro.cif, chain Ab (#1) with
fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score
= 342
RMSD between 63 pruned atom pairs is 0.737 angstroms; (across all 73 pairs:
2.555)
> matchmaker #2 to #1 & sel
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 monomerhcpro.cif, chain Ab (#1) with
fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score
= 342
RMSD between 63 pruned atom pairs is 0.737 angstroms; (across all 73 pairs:
2.555)
> matchmaker #2 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 monomerhcpro.cif, chain Ab (#1) with
fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score
= 1127.3
RMSD between 151 pruned atom pairs is 0.771 angstroms; (across all 261 pairs:
36.016)
> ui tool show "Command Line Interface"
> lighting intensity 0.45 ambientIntensity 0.14 fillIntensity 1 depthCue true
> shadows true multiShadow 64
> cartoon style (sel & coil) xsection oval
> cartoon style sel xsection barbell modeHelix default
> select add #2
4180 atoms, 4262 bonds, 530 residues, 2 models selected
> hide #!1 models
> color (#2 & sel) dim gray
> color (#2 & sel) gray
> color (#2 & sel) light gray
> hide #2 models
> select subtract #2
584 atoms, 594 bonds, 73 residues, 1 model selected
> show #2 models
> show #!1 models
> select add #2
4180 atoms, 4262 bonds, 530 residues, 2 models selected
> select subtract #2
584 atoms, 594 bonds, 73 residues, 1 model selected
> hide #2 models
> show #2 models
> select add #2
4180 atoms, 4262 bonds, 530 residues, 2 models selected
> hide #!1 models
> show #!1 models
> ui tool show "Color Actions"
> color sel pale violet red
> undo
> select subtract #2
584 atoms, 594 bonds, 73 residues, 1 model selected
> select add #1
2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected
> select subtract #1
Nothing selected
> select add #1
2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected
> color sel pale violet red
> select clear
> save "/Users/nezakoritnik/Desktop/Alphafold C.png" width 3000 height 2487
> supersample 3 transparentBackground true
> save /Users/nezakoritnik/Desktop/alphafoldC.cxs
> save "/Users/nezakoritnik/Desktop/AlphaFold C2.png" width 3000 height 2487
> supersample 3 transparentBackground true
No reference and/or match structure/chain chosen
> matchmaker #2 to #1 & sel
No 'to' model specified
> select #1/Ab:102
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/Ab:102-186
673 atoms, 684 bonds, 85 residues, 1 model selected
> matchmaker #2 to #1 & sel
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 monomerhcpro.cif, chain Ab (#1) with
fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score
= 397.4
RMSD between 60 pruned atom pairs is 0.699 angstroms; (across all 85 pairs:
11.855)
> matchmaker #2 to #1 & sel
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 monomerhcpro.cif, chain Ab (#1) with
fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score
= 397.4
RMSD between 60 pruned atom pairs is 0.699 angstroms; (across all 85 pairs:
11.855)
> matchmaker #2 to #1 & sel
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 monomerhcpro.cif, chain Ab (#1) with
fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score
= 397.4
RMSD between 60 pruned atom pairs is 0.699 angstroms; (across all 85 pairs:
11.855)
> matchmaker #2 to #1 & sel
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 monomerhcpro.cif, chain Ab (#1) with
fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score
= 397.4
RMSD between 60 pruned atom pairs is 0.699 angstroms; (across all 85 pairs:
11.855)
> matchmaker #2 to #1 & sel
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 monomerhcpro.cif, chain Ab (#1) with
fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score
= 397.4
RMSD between 60 pruned atom pairs is 0.699 angstroms; (across all 85 pairs:
11.855)
> matchmaker #2 to #1 & sel
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 monomerhcpro.cif, chain Ab (#1) with
fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score
= 397.4
RMSD between 60 pruned atom pairs is 0.699 angstroms; (across all 85 pairs:
11.855)
> matchmaker #2 to #1 & sel
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 monomerhcpro.cif, chain Ab (#1) with
fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score
= 397.4
RMSD between 60 pruned atom pairs is 0.699 angstroms; (across all 85 pairs:
11.855)
> select clear
> save "/Users/nezakoritnik/Desktop/Alphafold N.png" width 3000 height 2487
> supersample 3 transparentBackground true
> save "/Users/nezakoritnik/Desktop/Alphafold N2.png" width 3000 height 2487
> supersample 3 transparentBackground true
> hide #2 models
> show #2 models
> save /Users/nezakoritnik/Desktop/alphafoldN.cxs
> hide #2 models
> save /Users/nezakoritnik/Desktop/monomer.cxs
> save "/Users/nezakoritnik/Desktop/monomer 1.png" width 3000 height 2435
> supersample 3 transparentBackground true
> lighting intensity 0.45 ambientIntensity 0.14 fillIntensity 1 depthCue true
> shadows true multiShadow 0
> lighting intensity 0.45 ambientIntensity 0.14 fillIntensity 1 depthCue true
> shadows true multiShadow 64
> save "/Users/nezakoritnik/Desktop/monomer 2.png" width 3000 height 2435
> supersample 3 transparentBackground true
> show #2 models
> matchmaker #2 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 monomerhcpro.cif, chain Ab (#1) with
fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score
= 1127.3
RMSD between 151 pruned atom pairs is 0.771 angstroms; (across all 261 pairs:
36.016)
> hide #!1 models
> show #!1 models
> select add #1
2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected
> ui tool show "Color Actions"
> color sel pink
> hide #2 models
> select clear
> save "/Users/nezakoritnik/Desktop/monomer 1.1.png" width 3000 height 2435
> supersample 3 transparentBackground true
> save "/Users/nezakoritnik/Desktop/monomer 2.1.png" width 3000 height 2435
> supersample 3 transparentBackground true
> select #1/Ab:410-411
18 atoms, 18 bonds, 2 residues, 1 model selected
> select #1/Ab:410-457
386 atoms, 393 bonds, 48 residues, 1 model selected
Drag select of 1 residues
> select #1/Ab:343
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/Ab:343-457
904 atoms, 922 bonds, 115 residues, 1 model selected
> select #1/Ab:342
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/Ab:342-343
18 atoms, 18 bonds, 2 residues, 1 model selected
> select #1/Ab:342
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/Ab:342-457
916 atoms, 935 bonds, 116 residues, 1 model selected
> rainbow sel
> select clear
> rainbow #!1
> save "/Users/nezakoritnik/Desktop/monomer 1.png" width 3000 height 2435
> supersample 3
> save "/Users/nezakoritnik/Desktop/monomer 1.png" width 3000 height 2435
> supersample 3 transparentBackground true
> rotate 180
Unknown command: rotate 180
> rot 180
Unknown command: rot 180
> turn z 180
> turn y 180
> save "/Users/nezakoritnik/Desktop/monomer 2.png" width 3000 height 2435
> supersample 3 transparentBackground true
> select #1/Ab:293
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select #1/Ab:279
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> disulphides
Unknown command: disulphides
> show disulfides
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show /ss
> select #1/Ab:279@CA
1 atom, 1 residue, 1 model selected
> select #1/Ab:279@SG
1 atom, 1 residue, 1 model selected
> select #1/Ab:290
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/Ab:279@SG
1 atom, 1 residue, 1 model selected
> select add #1/Ab:293@SG
2 atoms, 2 residues, 1 model selected
> bond sel
Created 1 bond
> ui tool show "Side View"
> save /Users/nezakoritnik/Desktop/disulfid.png width 3000 height 2579
> supersample 3 transparentBackground true
> select clear
> save /Users/nezakoritnik/Desktop/disulfid.png width 3000 height 2579
> supersample 3 transparentBackground true
> select #1/Ab:180
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/Ab:180
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/Ab:181
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/Ab:182
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/Ab:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> color #1 byhetero
> save /Users/nezakoritnik/Desktop/monomer.cxs
> open /Users/nezakoritnik/Desktop/HCPro-struktura/NOVHCPro-
> Andreja/Rigidbodyrefine16/chains_filament16_real_space_refined.pdb
Summary of feedback from opening /Users/nezakoritnik/Desktop/HCPro-
struktura/NOVHCPro-
Andreja/Rigidbodyrefine16/chains_filament16_real_space_refined.pdb
---
warnings | Ignored bad PDB record found on line 379
SSBOND 1 CYS Aa 279 CYS Aa 293
Ignored bad PDB record found on line 380
SSBOND 2 CYS Ab 279 CYS Ab 293
Ignored bad PDB record found on line 381
SSBOND 3 CYS Ac 279 CYS Ac 293
Ignored bad PDB record found on line 382
SSBOND 4 CYS Ad 279 CYS Ad 293
Ignored bad PDB record found on line 383
SSBOND 5 CYS Ae 279 CYS Ae 293
19 messages similar to the above omitted
Chain information for chains_filament16_real_space_refined.pdb #3
---
Chain | Description
Aa Ab Ac Ad Ae Af Ag Ah Ai Aj Ak Al Am An Ao Ap Aq Ar As At Au Av Aw Ax | No description available
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!3 surfaces
> open /Users/nezakoritnik/Desktop/HCPro-struktura/NOVHCPro-Andreja/newPVA-
> HCPro_P130_J481.mrc
Opened newPVA-HCPro_P130_J481.mrc as #4, grid size 512,512,512, pixel 0.834,
shown at level 0.0803, step 2, values float32
> transparency 50
> color #4 #ebebebff models
> transparency 0
> transparency 50
> hide #!4 models
> lighting soft
> select #3/Aa
2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected
> color (#!3 & sel) red
> select clear
> save /Users/nezakoritnik/Desktop/interakcije1.png width 3000 height 2871
> supersample 3 transparentBackground true
> close #4
> save /Users/nezakoritnik/Desktop/interakcije.cxs
> open /Users/nezakoritnik/Desktop/HCPro-struktura/NOVHCPro-Andreja/newPVA-
> HCPro_P130_J481.mrc
Opened newPVA-HCPro_P130_J481.mrc as #4, grid size 512,512,512, pixel 0.834,
shown at level 0.0803, step 2, values float32
> select add #4
2 models selected
> transparency sel 50
> color #4 white models
> hide #!4 models
> show #!4 models
> select subtract #4
Nothing selected
> lighting soft
> color #4 #ebebebff models
> volume #4 step 1
> surface dust #4 size 8.34
> select add #4
2 models selected
> transparency sel 50
> select subtract #4
Nothing selected
> hide #!4 models
> show #!4 models
> select add #4
3 models selected
> color #4 #d6d6d6ff models
> transparency #4.1 70
> select subtract #4
Nothing selected
> save "/Users/nezakoritnik/Desktop/HCPro-struktura/NOVHCPro-
> Andreja/interakcije 1.1.cxs" includeMaps true
> save "/Users/nezakoritnik/Desktop/HCPro-struktura/NOVHCPro-
> Andreja/interakcije 1.1.png" width 3000 height 2871 supersample 3
> transparentBackground true
> hide #!4 models
> show #!4 models
> hide #!4 models
> save "/Users/nezakoritnik/Desktop/interakcije 2.png" width 3000 height 2605
> supersample 3 transparentBackground true
> show #!4 models
> color #4 darkgrey models
> save "/Users/nezakoritnik/Desktop/interakcije 1.1.png" width 3000 height
> 2605 supersample 3
> hide #!3 models
> hide #!4 models
> show #!3 models
> show #!4 models
> hide #!4 models
> hide #!3 surfaces
> style #!3 stick
Changed 49344 atom styles
> show #!3 cartoons
> hide #!3 atoms
> cartoon style #3 modeHelix tube sides 20
> show #!3 surfaces
> transparency #3 0
> ui tool show "Command Line Interface"
> split
Did not split monomerhcpro.cif, has only one piece
Did not split fold_2024_05_09_pva_hcpro_model_0.cif, has only one piece
Split chains_filament16_real_space_refined.pdb (#3) into 24 models
Chain information for chains_filament16_real_space_refined.pdb Aa #3.1
---
Chain | Description
Aa | No description available
Chain information for chains_filament16_real_space_refined.pdb Ab #3.2
---
Chain | Description
Ab | No description available
Chain information for chains_filament16_real_space_refined.pdb Ac #3.3
---
Chain | Description
Ac | No description available
Chain information for chains_filament16_real_space_refined.pdb Ad #3.4
---
Chain | Description
Ad | No description available
Chain information for chains_filament16_real_space_refined.pdb Ae #3.5
---
Chain | Description
Ae | No description available
Chain information for chains_filament16_real_space_refined.pdb Af #3.6
---
Chain | Description
Af | No description available
Chain information for chains_filament16_real_space_refined.pdb Ag #3.7
---
Chain | Description
Ag | No description available
Chain information for chains_filament16_real_space_refined.pdb Ah #3.8
---
Chain | Description
Ah | No description available
Chain information for chains_filament16_real_space_refined.pdb Ai #3.9
---
Chain | Description
Ai | No description available
Chain information for chains_filament16_real_space_refined.pdb Aj #3.10
---
Chain | Description
Aj | No description available
Chain information for chains_filament16_real_space_refined.pdb Ak #3.11
---
Chain | Description
Ak | No description available
Chain information for chains_filament16_real_space_refined.pdb Al #3.12
---
Chain | Description
Al | No description available
Chain information for chains_filament16_real_space_refined.pdb Am #3.13
---
Chain | Description
Am | No description available
Chain information for chains_filament16_real_space_refined.pdb An #3.14
---
Chain | Description
An | No description available
Chain information for chains_filament16_real_space_refined.pdb Ao #3.15
---
Chain | Description
Ao | No description available
Chain information for chains_filament16_real_space_refined.pdb Ap #3.16
---
Chain | Description
Ap | No description available
Chain information for chains_filament16_real_space_refined.pdb Aq #3.17
---
Chain | Description
Aq | No description available
Chain information for chains_filament16_real_space_refined.pdb Ar #3.18
---
Chain | Description
Ar | No description available
Chain information for chains_filament16_real_space_refined.pdb As #3.19
---
Chain | Description
As | No description available
Chain information for chains_filament16_real_space_refined.pdb At #3.20
---
Chain | Description
At | No description available
Chain information for chains_filament16_real_space_refined.pdb Au #3.21
---
Chain | Description
Au | No description available
Chain information for chains_filament16_real_space_refined.pdb Av #3.22
---
Chain | Description
Av | No description available
Chain information for chains_filament16_real_space_refined.pdb Aw #3.23
---
Chain | Description
Aw | No description available
Chain information for chains_filament16_real_space_refined.pdb Ax #3.24
---
Chain | Description
Ax | No description available
> show #!3.1-24 surfaces
> hide #!3 models
> show #!3 models
> hide #!3.2 models
> hide #!3.3 models
> hide #!3.4 models
> show #!3.4 models
> hide #!3.4 models
> hide #!3.5 models
> hide #!3.6 models
> hide #!3.7 models
> show #!3.7 models
> hide #!3.8 models
> hide #!3.7 models
> hide #!3.9 models
> hide #!3.10 models
> hide #!3.11 models
> hide #!3.12 models
> hide #!3.13 models
> hide #!3.14 models
> hide #!3.15 models
> hide #!3.16 models
> hide #!3.17 models
> hide #!3.18 models
> hide #!3.19 models
> hide #!3.20 models
> hide #!3.21 models
> hide #!3.22 models
> hide #!3.23 models
> hide #!3.24 models
> show #!3.7 models
> hide #!3.7 models
> show #!3.3 models
> hide #!3.3 models
> show #!3.4 models
> hide #!3.1,4 surfaces
> show #!3.1,4 surfaces
> hide #!3.1,4 surfaces
> hide #!3.4 models
> show #!3.3 models
> show #!3.1,3 surfaces
> hide #!3.3 models
> show #!3.8 models
> hide #!3.8 models
> show #!3.21 models
> hide #!3.21 models
> show #!3.2 models
> show #!3.11 models
> hide #!3.11 models
> show #!3.17 models
> hide #!3.17 models
> show #!3.17 models
> hide #!3.17 models
> hide #!3.2 models
> hide #!3.1 models
> show #!3.3 models
> show #!3.1 models
> show #!3.4 models
> hide #!3.3 models
> hide #!3.1,4 surfaces
> cartoon style #3.1,4#!3 modeHelix tube sides 20
> cartoon style (#3.1,4#!3 & coil) xsection oval
> cartoon style #3.1,4#!3 xsection barbell modeHelix default
> lighting intensity 0.45 ambientIntensity 0.14 fillIntensity 1 depthCue true
> shadows true multiShadow 64
> select add #3.1
2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected
> ui tool show "Color Actions"
> color sel pink
> select clear
> show #!3.1,4 atoms
> color #3.1,4#!3 byhetero
> ui mousemode right distance
> distance #3.4/Ad:135@OE1 #3.1/Aa:455@NH1
Distance between chains_filament16_real_space_refined.pdb Ad #3.4/Ad GLU 135
OE1 and chains_filament16_real_space_refined.pdb Aa #3.1/Aa ARG 455 NH1:
5.036Å
> hide #!3.1,4 atoms
> select #3.4/Ad:135
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:455
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> ui tool show "Color Actions"
> color sel lime
> select #3.4/Ad:126
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:413
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> distance #3.1/Aa:413@NZ #3.4/Ad:126@OG1
Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa LYS 413
NZ and chains_filament16_real_space_refined.pdb Ad #3.4/Ad THR 126 OG1: 3.203Å
> select clear
> hide #5.1 models
> save "/Users/nezakoritnik/Desktop/INTERFACE 1/od-cd.png" width 3000 height
> 2435 supersample 3 transparentBackground true
> save "/Users/nezakoritnik/Desktop/INTERFACE 1/od-cd.cxs"
> close #4
> hide #!3.1,4 atoms
> select #3.1/Aa:450
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.4/Ad:127
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.4/Ad:128
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> show sel atoms
> select clear
> hide #!3.1,4 atoms
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select #2/A:109
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:109-220
889 atoms, 905 bonds, 112 residues, 1 model selected
> select #2/A:260-261
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #2/A:260-325
506 atoms, 515 bonds, 66 residues, 1 model selected
> select #2/A:321-322
15 atoms, 15 bonds, 2 residues, 1 model selected
> select #2/A:209-322
892 atoms, 910 bonds, 114 residues, 1 model selected
> select #2/A:5
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:5-423
3296 atoms, 3363 bonds, 419 residues, 1 model selected
> select #2/A:158
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:158-260
831 atoms, 845 bonds, 103 residues, 1 model selected
> select #2/A:52-102
414 atoms, 421 bonds, 51 residues, 1 model selected
> select #2/A:1-102
805 atoms, 821 bonds, 102 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #3.1/Aa
Alignment identifier is 3.1/Aa
> ui tool show "Show Sequence Viewer"
> sequence chain #3.4/Ad
Alignment identifier is 3.4/Ad
> select #3.4/Ad:457
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3.4/Ad:298-457
994 atoms, 1015 bonds, 1 pseudobond, 126 residues, 2 models selected
> select #3.4/Ad:267-268
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #3.4/Ad:267-457
1226 atoms, 1250 bonds, 1 pseudobond, 157 residues, 2 models selected
> select #3.4/Ad:170
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.4/Ad:170-457
1502 atoms, 1527 bonds, 2 pseudobonds, 192 residues, 2 models selected
> select #3.4/Ad:146
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3.4/Ad:146-457
1689 atoms, 1717 bonds, 2 pseudobonds, 216 residues, 2 models selected
> cartoon hide (#!3.4 & sel)
> select #3.1/Aa:101-102
23 atoms, 24 bonds, 2 residues, 1 model selected
> select #3.1/Aa:101-145
367 atoms, 375 bonds, 45 residues, 1 model selected
> hide (#!3.1 & sel) target a
> cartoon hide (#!3.1 & sel)
> select #3.1/Aa:457
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3.1/Aa:298-457
994 atoms, 1015 bonds, 1 pseudobond, 126 residues, 2 models selected
> select #3.1/Aa:170-171
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #3.1/Aa:170-457
1502 atoms, 1527 bonds, 2 pseudobonds, 192 residues, 2 models selected
> hide (#!3.1 & sel) target a
> cartoon hide (#!3.1 & sel)
> show sel atoms
> hide sel atoms
> select clear
> show #!3.1,4 atoms
> undo
> select #3.4/Ad:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:163
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> distance #3.1/Aa:163@NH1 #3.4/Ad:117@OE1
Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa ARG 163
NH1 and chains_filament16_real_space_refined.pdb Ad #3.4/Ad GLU 117 OE1:
4.957Å
> ui tool show "Color Actions"
> color sel lime
> select #3.1/Aa:166
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:169
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.4/Ad:127
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:168
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:166
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3.1/Aa:167
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.1/Aa:168
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3.1/Aa:168-297
526 atoms, 529 bonds, 1 pseudobond, 68 residues, 2 models selected
> select #3.4/Ad:160
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3.4/Ad:160-252
253 atoms, 254 bonds, 1 pseudobond, 31 residues, 2 models selected
> cartoon (#!3.4 & sel)
> select #3.4/Ad:160
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3.4/Ad:101-160
473 atoms, 483 bonds, 60 residues, 1 model selected
> select
> #3.1/Aa:112-122,128-141,143-145,148-166,177-179,258-265,289-291,345-354,363-369,371-375,381-394,436-443,451-453
863 atoms, 865 bonds, 108 residues, 1 model selected
> select #3.1/Aa:168-297
526 atoms, 529 bonds, 1 pseudobond, 68 residues, 2 models selected
> select #3.1/Aa:146
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3.1/Aa:146-297
695 atoms, 701 bonds, 1 pseudobond, 90 residues, 2 models selected
> show sel cartoons
> select #3.4/Ad:457
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3.4/Ad
2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected
> show sel cartoons
> select clear
> select #3.1/Aa:101
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3.1/Aa:101-252
717 atoms, 729 bonds, 1 pseudobond, 90 residues, 2 models selected
> cartoon (#!3.1 & sel)
> select #3.4/Ad:169
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #3.4/Ad:170
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.4/Ad:170
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.4/Ad:168
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:171
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.4/Ad:170
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:170
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> hide #!3.1,4 atoms
> select #3.4/Ad:170
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:171
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:170
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:170
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/Aa:168
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:171
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> distance #3.4/Ad:170@OD1 #3.1/Aa:168@NH1
Distance between chains_filament16_real_space_refined.pdb Ad #3.4/Ad ASP 170
OD1 and chains_filament16_real_space_refined.pdb Aa #3.1/Aa ARG 168 NH1:
4.754Å
> color sel lime
> select clear
> ui tool show "Side View"
> save "/Users/nezakoritnik/Desktop/INTERFACE 1/zanka-zanka.cxs"
> save "/Users/nezakoritnik/Desktop/INTERFACE 1/zanka-zanka.png" width 3000
> height 2435 supersample 3 transparentBackground true
> open "/Users/nezakoritnik/Desktop/INTERFACE 1/od-cd.cxs"
Opened newPVA-HCPro_P130_J481.mrc as #4, grid size 512,512,512, pixel 0.834,
shown at level 0.0803, step 1, values float32
opened ChimeraX session
> save "/Users/nezakoritnik/Desktop/INTERFACE 1/od-cd.png" width 3000 height
> 2435 supersample 3 transparentBackground true
> hide #!3.1,4 atoms
> ui tool show "Show Sequence Viewer"
> sequence chain #3.1/Aa
Alignment identifier is 3.1/Aa
> select #3.1/Aa:457
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3.1/Aa:377-457
635 atoms, 649 bonds, 81 residues, 1 model selected
> select #3.1/Aa:273
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3.1/Aa:273-457
1181 atoms, 1205 bonds, 1 pseudobond, 151 residues, 2 models selected
> select #3.1/Aa:253
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.1/Aa:253-457
1339 atoms, 1363 bonds, 1 pseudobond, 171 residues, 2 models selected
> select #3.1/Aa:167
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.1/Aa:167-457
1528 atoms, 1553 bonds, 2 pseudobonds, 195 residues, 2 models selected
> select #3.1/Aa:175
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3.1/Aa:175-457
1460 atoms, 1485 bonds, 2 pseudobonds, 187 residues, 2 models selected
> cartoon hide (#!3.1 & sel)
> select #3.1/Aa:101
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3.1/Aa:101-140
333 atoms, 341 bonds, 40 residues, 1 model selected
> select #3.1/Aa:145
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3.1/Aa:101-145
367 atoms, 375 bonds, 45 residues, 1 model selected
> cartoon hide (#!3.1 & sel)
> ui tool show "Show Sequence Viewer"
> sequence chain #3.4/Ad
Alignment identifier is 3.4/Ad
> select #3.4/Ad:457
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3.4/Ad:253-457
1339 atoms, 1363 bonds, 1 pseudobond, 171 residues, 2 models selected
> select #3.4/Ad:167
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.4/Ad:167-457
1528 atoms, 1553 bonds, 2 pseudobonds, 195 residues, 2 models selected
> select #3.4/Ad:148
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.4/Ad:148-457
1677 atoms, 1705 bonds, 2 pseudobonds, 214 residues, 2 models selected
> hide sel cartoons
> select #3.1/Aa:166
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.4/Ad:130
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> distance #3.1/Aa:166@NH1 #3.4/Ad:130@OH
Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa ARG 166
NH1 and chains_filament16_real_space_refined.pdb Ad #3.4/Ad TYR 130 OH: 3.848Å
> select clear
> select #3.1/Aa:163
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.4/Ad:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:169
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> distance #3.1/Aa:169@OG1 #3.4/Ad:130@OH
Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa THR 169
OG1 and chains_filament16_real_space_refined.pdb Ad #3.4/Ad TYR 130 OH: 2.497Å
> select #3.1/Aa:170
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #3.1/Aa:171
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.4/Ad:127
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> distance #3.1/Aa:171@OD1 #3.4/Ad:127@NE2
Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa ASN 171
OD1 and chains_filament16_real_space_refined.pdb Ad #3.4/Ad GLN 127 NE2:
6.116Å
> hide sel atoms
> select #3.1/Aa:171
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/Aa:159
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.4/Ad:133
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.4/Ad:118
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.4/Ad:114
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:162
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:155
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.4/Ad:141
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3.4/Ad:140
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.1/Aa:158
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.4/Ad:137
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #3.4/Ad:140
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:154
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.4/Ad:137
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.4/Ad:137
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.4/Ad:111
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #3.4/Ad:136
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:161
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.4/Ad:136@CA
1 atom, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #3.4/Ad:136
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/Aa:162
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3.1/Aa:161
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.1/Aa:165
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.4/Ad:129
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.4/Ad:137
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.4/Ad:137
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.4/Ad:136
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.4/Ad:137
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #3.1/Aa:151
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> save "/Users/nezakoritnik/Desktop/INTERFACE 1/od-od.cxs"
> ui tool show "Side View"
> select #3.4/Ad:109
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> distance #3.4/Ad:109@OD1 #3.1/Aa:163@NH1
Distance between chains_filament16_real_space_refined.pdb Ad #3.4/Ad ASN 109
OD1 and chains_filament16_real_space_refined.pdb Aa #3.1/Aa ARG 163 NH1:
14.827Å
> ~distance #3.4/Ad:109@OD1 #3.1/Aa:163@NH1
> distance #3.1/Aa:163@NH1 #3.4/Ad:117@OE1
Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa ARG 163
NH1 and chains_filament16_real_space_refined.pdb Ad #3.4/Ad GLU 117 OE1:
4.957Å
> distance #3.4/Ad:109@OD1 #3.1/Aa:155@OG
Distance between chains_filament16_real_space_refined.pdb Ad #3.4/Ad ASN 109
OD1 and chains_filament16_real_space_refined.pdb Aa #3.1/Aa SER 155 OG: 3.725Å
> turn y 180
> select #3.4/Ad:129
7 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> turn y 180
> select clear
> save "/Users/nezakoritnik/Desktop/INTERFACE 1/od-od1.png" width 3000 height
> 2435 supersample 3 transparentBackground true
> turn y 180
> save "/Users/nezakoritnik/Desktop/INTERFACE 1/od-od1.png" width 3000 height
> 2435 supersample 3 transparentBackground true
> undo
> select clear
> color sel lime
> select clear
> save "/Users/nezakoritnik/Desktop/INTERFACE 1/od-od1.png" width 3000 height
> 2435 supersample 3 transparentBackground true
> turn y 180
> save "/Users/nezakoritnik/Desktop/INTERFACE 1/od-od2.png" width 3000 height
> 2435 supersample 3 transparentBackground true
> save "/Users/nezakoritnik/Desktop/INTERFACE 1/od-od.cxs"
> hide #!5 models
> select #3.4/Ad:101
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3.4/Ad
2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected
> show sel cartoons
> hide sel atoms
> select #3.1/Aa:456-457
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #3.1/Aa
2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected
> show sel cartoons
> hide sel atoms
> select clear
> save "/Users/nezakoritnik/Desktop/INTERFACE 1/celoten.cxs"
> save "/Users/nezakoritnik/Desktop/INTERFACE 1/celoten.png" width 3000 height
> 2435 supersample 3
> show #!3.3 models
> hide #!3.4 models
> hide #!3.1,3 surfaces
> select add #3.3
2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected
> ui tool show "Color Actions"
> color sel aquamarine
> color sel medium aquamarine
> color sel mint cream
> color sel pale turquoise
> show #!3.4 models
> ui tool show "Color Actions"
> color #3.3 #a4c4b3ff
> color #3.3 #dbfdefff
> color #3.3 #cdf4e1ff
> hide #!3.4 models
> select clear
> save "/Users/nezakoritnik/Desktop/INTERFACE 2/celoten.png" width 3000 height
> 2435 supersample 3
> show #!3.4 models
> hide #!3.3 models
> select clear
> select #3.4/Ad:450
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:126
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:127
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #3.1/Aa:128
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.4/Ad:453
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:164
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:157
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:132
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!3.3 models
> hide #!3.4 models
> select #3.1/Aa:457
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3.1/Aa:169-457
1509 atoms, 1534 bonds, 2 pseudobonds, 193 residues, 2 models selected
> hide sel cartoons
> ui tool show "Show Sequence Viewer"
> sequence chain #3.3/Ac
Alignment identifier is 3.3/Ac
> select #3.3/Ac:101
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3.3/Ac:101-183
666 atoms, 678 bonds, 83 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select clear
> hide #!3.1,3 atoms
> select #3.1/Aa:113
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #3.1/Aa:106
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.3/Ac:362
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> color #3.1,3#!3 byhetero
> distance #3.1/Aa:106@NH1 #3.3/Ac:362@OD2
Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa ARG 106
NH1 and chains_filament16_real_space_refined.pdb Ac #3.3/Ac ASP 362 OD2:
2.728Å
> distance #3.3/Ac:362@OD2 #3.1/Aa:106@NH1
Distance already exists; modify distance properties with 'distance style'
> show #!5 models
> color sel lime
> select #3.1/Aa:145
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> show sel atoms
> select #3.3/Ac:357
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.3/Ac:358
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.3/Ac:359
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.3/Ac:360
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select clear
> select #3.3/Ac:358
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/Aa:145
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.3/Ac:359
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.3/Ac:357
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/Aa:115
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.3/Ac:389
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> ui mousemode right distance
> distance #3.1/Aa:115@OH #3.3/Ac:389@OG
Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa TYR 115
OH and chains_filament16_real_space_refined.pdb Ac #3.3/Ac SER 389 OG: 2.696Å
> select #3.1/Aa:116
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.3/Ac:374
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> distance #3.1/Aa:116@NH1 #3.3/Ac:374@OD2
Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa ARG 116
NH1 and chains_filament16_real_space_refined.pdb Ac #3.3/Ac ASP 374 OD2:
3.301Å
> color sel lime
> select #3.1/Aa:120
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.3/Ac:445
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> distance #3.1/Aa:120@NZ #3.3/Ac:445@OD1
Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa LYS 120
NZ and chains_filament16_real_space_refined.pdb Ac #3.3/Ac ASN 445 OD1: 3.904Å
> select #3.1/Aa:138
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.3/Ac:437
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:135
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.3/Ac:440
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.3/Ac:437
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3.3/Ac:437
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/Aa:135
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.3/Ac:393
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3.1/Aa:142
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.3/Ac:394
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:142
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/Aa:141
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.3/Ac:390
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:142
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:119
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.3/Ac:386
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.3/Ac:390
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.3/Ac:440
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.3/Ac:443
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> cartoon style (#!3.3 & sel) modeHelix tube sides 20
> cartoon style (#!3.3 & sel & coil) xsection oval
> cartoon style (#!3.3 & sel) xsection barbell modeHelix default
> select clear
> select #3.1/Aa:138
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> turn y 180
> save "/Users/nezakoritnik/Desktop/INTERFACE 2/interface1.png" width 3000
> height 2435 supersample 3 transparentBackground true
> turn y 180
> save "/Users/nezakoritnik/Desktop/INTERFACE 2/interface2.png" width 3000
> height 2435 supersample 3 transparentBackground true
> save "/Users/nezakoritnik/Desktop/INTERFACE 2/interface.cxs"
> turn y 180
> save "/Users/nezakoritnik/Desktop/INTERFACE 2/interface11.png" width 3000
> height 2435 supersample 3 transparentBackground true
> turn y 180
> save "/Users/nezakoritnik/Desktop/INTERFACE 2/interface 21.png" width 3000
> height 2435 supersample 3 transparentBackground true
> open "/Users/nezakoritnik/Desktop/INTERFACE 2/interface.cxs"
Opened newPVA-HCPro_P130_J481.mrc as #4, grid size 512,512,512, pixel 0.834,
shown at level 0.0803, step 1, values float32
opened ChimeraX session
> close #4
> show #!3.2 models
> ui tool show "Side View"
> hide #!3.1 models
> show #!3.1 models
> hide #!3.2 models
> show #!3.5 models
> hide #!3.5 models
> show #!3.5 models
> hide #!3.5 models
> show #!3.7 models
> hide #!3.7 models
> show #!3.9 models
> show #!3.8 models
> hide #!3.8 models
> hide #!3.9 models
> show #!3.10 models
> hide #!3.10 models
> show #!3.11 models
> show #!3.12 models
> hide #!3.11 models
> hide #!3.12 models
> show #!3.14 models
> hide #!3.14 models
> show #!3.15 models
> hide #!3.15 models
> show #!3.16 models
> hide #!3.16 models
> show #!3.17 models
> hide #!3.17 models
> show #!3.20 models
> hide #!3.20 models
> show #!3.20 models
> hide #!3.20 models
> show #!3.20 models
> hide #!3.20 models
> show #!3.20 models
> hide #!3.20 models
> show #!3.21 models
> hide #!3.21 models
> show #!3.21 models
> hide #!3.21 models
> show #!3.22 models
> hide #!3.22 models
> show #!3.21 models
> hide #!3.21 models
> select #3.3/Ac:407-457
409 atoms, 416 bonds, 51 residues, 1 model selected
> select #3.3/Ac
2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected
> show sel cartoons
> select #3.1/Aa:457
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3.1/Aa
2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected
> show sel cartoons
> show #!3.21 models
> hide sel surfaces
> select clear
> hide #!3.1,3,21 surfaces
> color #3.21 #e0fef3ff
> color #3.21 #c8e7d8ff
> cartoon style (#3.1,3,21#!3,5 & coil) xsection oval
> cartoon style #3.1,3,21#!3,5 xsection barbell modeHelix default
> hide #!3.3 models
> hide #!3.1,21 atoms
> save "/Users/nezakoritnik/Desktop/INTERFACE 3/celotna.png" width 3000 height
> 2435 supersample 3 transparentBackground true
> save "/Users/nezakoritnik/Desktop/INTERFACE 3/celotna.cxs"
> select #3.1/Aa:265
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:261
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:258
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.21/Au:254
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:254
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.21/Au:258
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.21/Au:261
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.21/Au:265
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:457
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3.1/Aa:298-457
994 atoms, 1015 bonds, 1 pseudobond, 126 residues, 2 models selected
> cartoon hide (#!3.1 & sel)
> select #3.1/Aa:297
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.1/Aa:270-297
213 atoms, 215 bonds, 28 residues, 1 model selected
> select #3.1/Aa:272
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3.1/Aa:272-297
196 atoms, 198 bonds, 26 residues, 1 model selected
> surface hidePatches (#!3.1 & sel)
> ui tool show "Show Sequence Viewer"
> sequence chain #3.21/Au
Alignment identifier is 3.21/Au
> select #3.21/Au:449-457
77 atoms, 78 bonds, 9 residues, 1 model selected
> select #3.21/Au:272-457
1190 atoms, 1214 bonds, 1 pseudobond, 152 residues, 2 models selected
> cartoon hide (#!3.21 & sel)
> select #3.21/Au:189
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #3.21/Au:101-189
709 atoms, 722 bonds, 89 residues, 1 model selected
> cartoon hide (#!3.21 & sel)
> select #3.1/Aa:189
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #3.1/Aa:101-189
709 atoms, 722 bonds, 89 residues, 1 model selected
> cartoon hide (#!3.1 & sel)
> select #3.1/Aa:281-282
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #3.1/Aa:281-297
132 atoms, 134 bonds, 17 residues, 1 model selected
> select #3.1/Aa:272
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3.1/Aa:272-297
196 atoms, 198 bonds, 26 residues, 1 model selected
> cartoon hide (#!3.1 & sel)
> select #3.1/Aa:266
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3.1/Aa:266-271
45 atoms, 44 bonds, 6 residues, 1 model selected
> hide (#!3.1 & sel) target a
> select #3.21/Au:266
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3.21/Au:266-275
75 atoms, 74 bonds, 10 residues, 1 model selected
> select #3.21/Au:267-268
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #3.21/Au:267-284
128 atoms, 127 bonds, 18 residues, 1 model selected
> cartoon hide (#!3.21 & sel)
> select #3.1/Aa:267
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3.1/Aa:267-278
87 atoms, 86 bonds, 12 residues, 1 model selected
> cartoon hide (#!3.1 & sel)
> save "/Users/nezakoritnik/Desktop/INTERFACE 3/interface.cxs"
> save "/Users/nezakoritnik/Desktop/INTERFACE 3/interface.png" width 3000
> height 2435 supersample 3 transparentBackground true
> undo
> surface hidePatches (#!3.1 & sel)
> select #3.1/Aa:457
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3.1/Aa
2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected
> show sel cartoons
> select #3.21/Au:457
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3.21/Au
2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected
> show sel cartoons
> ui tool show "Model Panel"
> show #!3.2 models
> show sel surfaces
> select clear
> show #!3.1-2,21 surfaces
> hide #!3.1-2,21 surfaces
> ui tool show "Show Sequence Viewer"
> sequence chain #3.2/Ab
Alignment identifier is 3.2/Ab
> select #3.2/Ab:105
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3.2/Ab:105-386
1462 atoms, 1484 bonds, 2 pseudobonds, 186 residues, 2 models selected
> select #3.2/Ab:386-387
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #3.2/Ab:101-387
1507 atoms, 1532 bonds, 2 pseudobonds, 191 residues, 2 models selected
> select #3.2/Ab:101
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3.2/Ab:101
12 atoms, 12 bonds, 1 residue, 1 model selected
> color #3.2 #daf6e9ff
> color #3.2 #d4efe3ff
> select add #3.2
2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 5 models selected
> select subtract #3.2
1 model selected
> hide #!3.21 models
> hide #!3.1-2 atoms
> select #3.1/Aa:173
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.2/Ab:285
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> hide #!3.1-2 atoms
> cartoon style (#3.1-2#!3,5 & coil) xsection oval
> cartoon style #3.1-2#!3,5 xsection barbell modeHelix default
> ui tool show "Side View"
> save "/Users/nezakoritnik/Desktop/INTERFACE 4/celotna.png" width 3000 height
> 2435 supersample 3 transparentBackground true
> save "/Users/nezakoritnik/Desktop/INTERFACE 4/celotna.cxs"
> select #3.1/Aa:173
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.2/Ab:284
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> show sel atoms
> select clear
> color #3.1-2#!3,5 byhetero
> select #3.2/Ab:285
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:163
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.2/Ab:120
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3.2/Ab:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> distance #3.2/Ab:117@OE2 #3.1/Aa:163@NH1
Distance between chains_filament16_real_space_refined.pdb Ab #3.2/Ab GLU 117
OE2 and chains_filament16_real_space_refined.pdb Aa #3.1/Aa ARG 163 NH1:
5.233Å
> show #5.1 models
> hide #5.1 models
> ui tool show "Color Actions"
> color sel lime
> select #3.1/Aa:173@NZ
1 atom, 1 residue, 1 model selected
> select clear
> select #3.1/Aa:173@NZ
1 atom, 1 residue, 1 model selected
> select #3.2/Ab:284@OD2
1 atom, 1 residue, 1 model selected
> select #3.1/Aa:173@NZ
1 atom, 1 residue, 1 model selected
> select clear
> select #3.2/Ab:284@OD2
1 atom, 1 residue, 1 model selected
> select #3.1/Aa:173@NZ
1 atom, 1 residue, 1 model selected
> select #3.2/Ab:284@OD2
1 atom, 1 residue, 1 model selected
> select add #3.1/Aa:173@NZ
2 atoms, 2 residues, 3 models selected
> select subtract #3.2/Ab:284@OD2
1 atom, 1 residue, 3 models selected
> select #3.1/Aa:173@NZ
1 atom, 1 residue, 1 model selected
Drag select of 1 atoms
> select #3.1/Aa:173@NZ
1 atom, 1 residue, 1 model selected
> select #3.2/Ab:284@OD2
1 atom, 1 residue, 1 model selected
> select #3.1/Aa:173@NZ
1 atom, 1 residue, 1 model selected
> select clear
> select #3.1/Aa:173@NZ
1 atom, 1 residue, 1 model selected
> select #3.2/Ab:284@OD2
1 atom, 1 residue, 1 model selected
> select clear
> select #3.1/Aa:173@NZ
1 atom, 1 residue, 1 model selected
> distance #3.1/Aa:173@NZ #3.2/Ab:284@OD2
Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa LYS 173
NZ and chains_filament16_real_space_refined.pdb Ab #3.2/Ab ASP 284 OD2: 3.248Å
> distance #3.1/Aa:173@NZ #3.2/Ab:285@OD1
Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa LYS 173
NZ and chains_filament16_real_space_refined.pdb Ab #3.2/Ab ASN 285 OD1: 3.099Å
> color sel lime
> select #3.2/Ab:187
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> show sel atoms
> select #3.1/Aa:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> ui mousemode right distance
> distance #3.1/Aa:268@OE2 #3.2/Ab:187@NZ
Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa GLU 268
OE2 and chains_filament16_real_space_refined.pdb Ab #3.2/Ab LYS 187 NZ: 5.543Å
> select clear
> color sel lime
> select #3.2/Ab:286
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:276
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:275
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:274
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:273
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:277
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:273
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3.1/Aa:272
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:271
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:272
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3.2/Ab:287
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.2/Ab:288
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.2/Ab:289
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
Drag select of 1 residues
> select #3.2/Ab:290
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #3.2/Ab:289
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #3.2/Ab:288
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #3.2/Ab:287
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.2/Ab:286@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #3.2/Ab:286
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/Aa:277
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/Aa:276
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/Aa:275
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/Aa:274
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> hide sel atoms
> select #3.2/Ab:437
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:271
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/Aa:272
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #3.1/Aa:411
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:273
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/Aa:271
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.2/Ab:288
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #3.2/Ab:289
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #3.2/Ab:286
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> show sel atoms
> select #3.2/Ab:289
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.2/Ab:288
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.2/Ab:287
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #3.2/Ab:288
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #3.2/Ab:289
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.2/Ab:286
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> distance #3.2/Ab:437@NH2 #3.1/Aa:411@OD2
Distance between chains_filament16_real_space_refined.pdb Ab #3.2/Ab ARG 437
NH2 and chains_filament16_real_space_refined.pdb Aa #3.1/Aa ASP 411 OD2:
7.180Å
> show #5.1 models
> hide #5.1 models
> select clear
> color sel lime
> select #3.1/Aa:277
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #3.1/Aa:413
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> show sel atoms
> hide sel atoms
> select #3.1/Aa:271
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> save "/Users/nezakoritnik/Desktop/INTERFACE 4/interakcijska površina.cxs"
> save "/Users/nezakoritnik/Desktop/INTERFACE 4/interakcijska povrina.png"
> width 3000 height 2435 supersample 3 transparentBackground true
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/nezakoritnik/Desktop/INTERFACE 4/interakcijska površina.cxs"
Log from Wed Jan 29 07:29:35 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/nezakoritnik/Desktop/INTERFACE 2/interface.cxs"
Opened newPVA-HCPro_P130_J481.mrc as #4, grid size 512,512,512, pixel 0.834,
shown at level 0.0803, step 1, values float32
Log from Tue Jan 28 14:16:05 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/nezakoritnik/Desktop/INTERFACE 1/od-cd.cxs"
Opened newPVA-HCPro_P130_J481.mrc as #4, grid size 512,512,512, pixel 0.834,
shown at level 0.0803, step 1, values float32
Log from Tue Jan 28 10:12:17 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/nezakoritnik/Desktop/HCPro-struktura/monomerhcpro.cif
Summary of feedback from opening /Users/nezakoritnik/Desktop/HCPro-
struktura/monomerhcpro.cif
---
warnings | Unknown polymer entity '1' on line 131
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for monomerhcpro.cif #1
---
Chain | Description
Ab | No description available
> set bgColor white
> open "/Users/nezakoritnik/Documents/REZULTATI/Bioinformatske
> analize/AlphaFold/ALFAFOLD3/PVA-
> HCPro_2024_05_09_pva_hcpro/fold_2024_05_09_pva_hcpro_model_0.cif"
Chain information for fold_2024_05_09_pva_hcpro_model_0.cif #2
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #2 to #1
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 monomerhcpro.cif, chain Ab (#1) with
fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score
= 1127.3
RMSD between 151 pruned atom pairs is 0.771 angstroms; (across all 261 pairs:
36.016)
> ui tool show Matchmaker
> ui tool show "Show Sequence Viewer"
> sequence chain #1/Ab
Alignment identifier is 1/Ab
> select #1/Ab:102
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/Ab:102-174
584 atoms, 594 bonds, 73 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #2 to #1 & sel
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 monomerhcpro.cif, chain Ab (#1) with
fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score
= 342
RMSD between 63 pruned atom pairs is 0.737 angstroms; (across all 73 pairs:
2.555)
> matchmaker #2 to #1 & sel
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 monomerhcpro.cif, chain Ab (#1) with
fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score
= 342
RMSD between 63 pruned atom pairs is 0.737 angstroms; (across all 73 pairs:
2.555)
> matchmaker #2 to #1
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 monomerhcpro.cif, chain Ab (#1) with
fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score
= 1127.3
RMSD between 151 pruned atom pairs is 0.771 angstroms; (across all 261 pairs:
36.016)
> ui tool show "Command Line Interface"
> lighting intensity 0.45 ambientIntensity 0.14 fillIntensity 1 depthCue true
> shadows true multiShadow 64
> cartoon style (sel & coil) xsection oval
> cartoon style sel xsection barbell modeHelix default
> select add #2
4180 atoms, 4262 bonds, 530 residues, 2 models selected
> hide #!1 models
> color (#2 & sel) dim gray
> color (#2 & sel) gray
> color (#2 & sel) light gray
> hide #2 models
> select subtract #2
584 atoms, 594 bonds, 73 residues, 1 model selected
> show #2 models
> show #!1 models
> select add #2
4180 atoms, 4262 bonds, 530 residues, 2 models selected
> select subtract #2
584 atoms, 594 bonds, 73 residues, 1 model selected
> hide #2 models
> show #2 models
> select add #2
4180 atoms, 4262 bonds, 530 residues, 2 models selected
> hide #!1 models
> show #!1 models
> ui tool show "Color Actions"
> color sel pale violet red
> undo
> select subtract #2
584 atoms, 594 bonds, 73 residues, 1 model selected
> select add #1
2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected
> select subtract #1
Nothing selected
> select add #1
2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected
> color sel pale violet red
> select clear
> save "/Users/nezakoritnik/Desktop/Alphafold C.png" width 3000 height 2487
> supersample 3 transparentBackground true
> save /Users/nezakoritnik/Desktop/alphafoldC.cxs
> save "/Users/nezakoritnik/Desktop/AlphaFold C2.png" width 3000 height 2487
> supersample 3 transparentBackground true
No reference and/or match structure/chain chosen
> matchmaker #2 to #1 & sel
No 'to' model specified
> select #1/Ab:102
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/Ab:102-186
673 atoms, 684 bonds, 85 residues, 1 model selected
> matchmaker #2 to #1 & sel
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 monomerhcpro.cif, chain Ab (#1) with
fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score
= 397.4
RMSD between 60 pruned atom pairs is 0.699 angstroms; (across all 85 pairs:
11.855)
> matchmaker #2 to #1 & sel
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 monomerhcpro.cif, chain Ab (#1) with
fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score
= 397.4
RMSD between 60 pruned atom pairs is 0.699 angstroms; (across all 85 pairs:
11.855)
> matchmaker #2 to #1 & sel
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 monomerhcpro.cif, chain Ab (#1) with
fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score
= 397.4
RMSD between 60 pruned atom pairs is 0.699 angstroms; (across all 85 pairs:
11.855)
> matchmaker #2 to #1 & sel
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 monomerhcpro.cif, chain Ab (#1) with
fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score
= 397.4
RMSD between 60 pruned atom pairs is 0.699 angstroms; (across all 85 pairs:
11.855)
> matchmaker #2 to #1 & sel
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 monomerhcpro.cif, chain Ab (#1) with
fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score
= 397.4
RMSD between 60 pruned atom pairs is 0.699 angstroms; (across all 85 pairs:
11.855)
> matchmaker #2 to #1 & sel
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 monomerhcpro.cif, chain Ab (#1) with
fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score
= 397.4
RMSD between 60 pruned atom pairs is 0.699 angstroms; (across all 85 pairs:
11.855)
> matchmaker #2 to #1 & sel
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 monomerhcpro.cif, chain Ab (#1) with
fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score
= 397.4
RMSD between 60 pruned atom pairs is 0.699 angstroms; (across all 85 pairs:
11.855)
> select clear
> save "/Users/nezakoritnik/Desktop/Alphafold N.png" width 3000 height 2487
> supersample 3 transparentBackground true
> save "/Users/nezakoritnik/Desktop/Alphafold N2.png" width 3000 height 2487
> supersample 3 transparentBackground true
> hide #2 models
> show #2 models
> save /Users/nezakoritnik/Desktop/alphafoldN.cxs
> hide #2 models
> save /Users/nezakoritnik/Desktop/monomer.cxs
> save "/Users/nezakoritnik/Desktop/monomer 1.png" width 3000 height 2435
> supersample 3 transparentBackground true
> lighting intensity 0.45 ambientIntensity 0.14 fillIntensity 1 depthCue true
> shadows true multiShadow 0
> lighting intensity 0.45 ambientIntensity 0.14 fillIntensity 1 depthCue true
> shadows true multiShadow 64
> save "/Users/nezakoritnik/Desktop/monomer 2.png" width 3000 height 2435
> supersample 3 transparentBackground true
> show #2 models
> matchmaker #2 to #1
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 monomerhcpro.cif, chain Ab (#1) with
fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score
= 1127.3
RMSD between 151 pruned atom pairs is 0.771 angstroms; (across all 261 pairs:
36.016)
> hide #!1 models
> show #!1 models
> select add #1
2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected
> ui tool show "Color Actions"
> color sel pink
> hide #2 models
> select clear
> save "/Users/nezakoritnik/Desktop/monomer 1.1.png" width 3000 height 2435
> supersample 3 transparentBackground true
> save "/Users/nezakoritnik/Desktop/monomer 2.1.png" width 3000 height 2435
> supersample 3 transparentBackground true
> select #1/Ab:410-411
18 atoms, 18 bonds, 2 residues, 1 model selected
> select #1/Ab:410-457
386 atoms, 393 bonds, 48 residues, 1 model selected
Drag select of 1 residues
> select #1/Ab:343
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/Ab:343-457
904 atoms, 922 bonds, 115 residues, 1 model selected
> select #1/Ab:342
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/Ab:342-343
18 atoms, 18 bonds, 2 residues, 1 model selected
> select #1/Ab:342
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/Ab:342-457
916 atoms, 935 bonds, 116 residues, 1 model selected
> rainbow sel
> select clear
> rainbow #!1
> save "/Users/nezakoritnik/Desktop/monomer 1.png" width 3000 height 2435
> supersample 3
> save "/Users/nezakoritnik/Desktop/monomer 1.png" width 3000 height 2435
> supersample 3 transparentBackground true
> rotate 180
Unknown command: rotate 180
> rot 180
Unknown command: rot 180
> turn z 180
[Repeated 1 time(s)]
> turn y 180
> save "/Users/nezakoritnik/Desktop/monomer 2.png" width 3000 height 2435
> supersample 3 transparentBackground true
> select #1/Ab:293
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select #1/Ab:279
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 2 time(s)]
> color sel byhetero
> disulphides
Unknown command: disulphides
> show disulfides
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show /ss
> select #1/Ab:279@CA
1 atom, 1 residue, 1 model selected
> select #1/Ab:279@SG
1 atom, 1 residue, 1 model selected
> select #1/Ab:290
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/Ab:279@SG
1 atom, 1 residue, 1 model selected
> select add #1/Ab:293@SG
2 atoms, 2 residues, 1 model selected
> bond sel
Created 1 bond
> ui tool show "Side View"
> save /Users/nezakoritnik/Desktop/disulfid.png width 3000 height 2579
> supersample 3 transparentBackground true
> select clear
> save /Users/nezakoritnik/Desktop/disulfid.png width 3000 height 2579
> supersample 3 transparentBackground true
> select #1/Ab:180
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/Ab:180
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/Ab:181
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/Ab:182
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/Ab:183
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> color #1 byhetero
> save /Users/nezakoritnik/Desktop/monomer.cxs
> open /Users/nezakoritnik/Desktop/HCPro-struktura/NOVHCPro-
> Andreja/Rigidbodyrefine16/chains_filament16_real_space_refined.pdb
Summary of feedback from opening /Users/nezakoritnik/Desktop/HCPro-
struktura/NOVHCPro-
Andreja/Rigidbodyrefine16/chains_filament16_real_space_refined.pdb
---
warnings | Ignored bad PDB record found on line 379
SSBOND 1 CYS Aa 279 CYS Aa 293
Ignored bad PDB record found on line 380
SSBOND 2 CYS Ab 279 CYS Ab 293
Ignored bad PDB record found on line 381
SSBOND 3 CYS Ac 279 CYS Ac 293
Ignored bad PDB record found on line 382
SSBOND 4 CYS Ad 279 CYS Ad 293
Ignored bad PDB record found on line 383
SSBOND 5 CYS Ae 279 CYS Ae 293
19 messages similar to the above omitted
Chain information for chains_filament16_real_space_refined.pdb #3
---
Chain | Description
Aa Ab Ac Ad Ae Af Ag Ah Ai Aj Ak Al Am An Ao Ap Aq Ar As At Au Av Aw Ax | No description available
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!3 surfaces
> open /Users/nezakoritnik/Desktop/HCPro-struktura/NOVHCPro-Andreja/newPVA-
> HCPro_P130_J481.mrc
Opened newPVA-HCPro_P130_J481.mrc as #4, grid size 512,512,512, pixel 0.834,
shown at level 0.0803, step 2, values float32
> transparency 50
> color #4 #ebebebff models
> transparency 0
> transparency 50
> hide #!4 models
> lighting soft
> select #3/Aa
2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected
> color (#!3 & sel) red
> select clear
> save /Users/nezakoritnik/Desktop/interakcije1.png width 3000 height 2871
> supersample 3 transparentBackground true
> close #4
> save /Users/nezakoritnik/Desktop/interakcije.cxs
> open /Users/nezakoritnik/Desktop/HCPro-struktura/NOVHCPro-Andreja/newPVA-
> HCPro_P130_J481.mrc
Opened newPVA-HCPro_P130_J481.mrc as #4, grid size 512,512,512, pixel 0.834,
shown at level 0.0803, step 2, values float32
> select add #4
2 models selected
> transparency sel 50
> color #4 white models
> hide #!4 models
> show #!4 models
> select subtract #4
Nothing selected
> lighting soft
> color #4 #ebebebff models
> volume #4 step 1
> surface dust #4 size 8.34
> select add #4
2 models selected
> transparency sel 50
> select subtract #4
Nothing selected
> hide #!4 models
> show #!4 models
> select add #4
3 models selected
> color #4 #d6d6d6ff models
> transparency #4.1 70
> select subtract #4
Nothing selected
> save "/Users/nezakoritnik/Desktop/HCPro-struktura/NOVHCPro-
> Andreja/interakcije 1.1.cxs" includeMaps true
> save "/Users/nezakoritnik/Desktop/HCPro-struktura/NOVHCPro-
> Andreja/interakcije 1.1.png" width 3000 height 2871 supersample 3
> transparentBackground true
> hide #!4 models
> show #!4 models
> hide #!4 models
> save "/Users/nezakoritnik/Desktop/interakcije 2.png" width 3000 height 2605
> supersample 3 transparentBackground true
> show #!4 models
> color #4 darkgrey models
> save "/Users/nezakoritnik/Desktop/interakcije 1.1.png" width 3000 height
> 2605 supersample 3
> hide #!3 models
> hide #!4 models
> show #!3 models
> show #!4 models
> hide #!4 models
> hide #!3 surfaces
> style #!3 stick
Changed 49344 atom styles
> show #!3 cartoons
> hide #!3 atoms
> cartoon style #3 modeHelix tube sides 20
> show #!3 surfaces
[Repeated 5 time(s)]
> transparency #3 0
> ui tool show "Command Line Interface"
> split
Did not split monomerhcpro.cif, has only one piece
Did not split fold_2024_05_09_pva_hcpro_model_0.cif, has only one piece
Split chains_filament16_real_space_refined.pdb (#3) into 24 models
Chain information for chains_filament16_real_space_refined.pdb Aa #3.1
---
Chain | Description
Aa | No description available
Chain information for chains_filament16_real_space_refined.pdb Ab #3.2
---
Chain | Description
Ab | No description available
Chain information for chains_filament16_real_space_refined.pdb Ac #3.3
---
Chain | Description
Ac | No description available
Chain information for chains_filament16_real_space_refined.pdb Ad #3.4
---
Chain | Description
Ad | No description available
Chain information for chains_filament16_real_space_refined.pdb Ae #3.5
---
Chain | Description
Ae | No description available
Chain information for chains_filament16_real_space_refined.pdb Af #3.6
---
Chain | Description
Af | No description available
Chain information for chains_filament16_real_space_refined.pdb Ag #3.7
---
Chain | Description
Ag | No description available
Chain information for chains_filament16_real_space_refined.pdb Ah #3.8
---
Chain | Description
Ah | No description available
Chain information for chains_filament16_real_space_refined.pdb Ai #3.9
---
Chain | Description
Ai | No description available
Chain information for chains_filament16_real_space_refined.pdb Aj #3.10
---
Chain | Description
Aj | No description available
Chain information for chains_filament16_real_space_refined.pdb Ak #3.11
---
Chain | Description
Ak | No description available
Chain information for chains_filament16_real_space_refined.pdb Al #3.12
---
Chain | Description
Al | No description available
Chain information for chains_filament16_real_space_refined.pdb Am #3.13
---
Chain | Description
Am | No description available
Chain information for chains_filament16_real_space_refined.pdb An #3.14
---
Chain | Description
An | No description available
Chain information for chains_filament16_real_space_refined.pdb Ao #3.15
---
Chain | Description
Ao | No description available
Chain information for chains_filament16_real_space_refined.pdb Ap #3.16
---
Chain | Description
Ap | No description available
Chain information for chains_filament16_real_space_refined.pdb Aq #3.17
---
Chain | Description
Aq | No description available
Chain information for chains_filament16_real_space_refined.pdb Ar #3.18
---
Chain | Description
Ar | No description available
Chain information for chains_filament16_real_space_refined.pdb As #3.19
---
Chain | Description
As | No description available
Chain information for chains_filament16_real_space_refined.pdb At #3.20
---
Chain | Description
At | No description available
Chain information for chains_filament16_real_space_refined.pdb Au #3.21
---
Chain | Description
Au | No description available
Chain information for chains_filament16_real_space_refined.pdb Av #3.22
---
Chain | Description
Av | No description available
Chain information for chains_filament16_real_space_refined.pdb Aw #3.23
---
Chain | Description
Aw | No description available
Chain information for chains_filament16_real_space_refined.pdb Ax #3.24
---
Chain | Description
Ax | No description available
> show #!3.1-24 surfaces
> hide #!3 models
> show #!3 models
> hide #!3.2 models
> hide #!3.3 models
> hide #!3.4 models
> show #!3.4 models
> hide #!3.4 models
> hide #!3.5 models
> hide #!3.6 models
> hide #!3.7 models
> show #!3.7 models
> hide #!3.8 models
> hide #!3.7 models
> hide #!3.9 models
> hide #!3.10 models
> hide #!3.11 models
> hide #!3.12 models
> hide #!3.13 models
> hide #!3.14 models
> hide #!3.15 models
> hide #!3.16 models
> hide #!3.17 models
> hide #!3.18 models
> hide #!3.19 models
> hide #!3.20 models
> hide #!3.21 models
> hide #!3.22 models
> hide #!3.23 models
> hide #!3.24 models
> show #!3.7 models
> hide #!3.7 models
> show #!3.3 models
> hide #!3.3 models
> show #!3.4 models
> hide #!3.1,4 surfaces
> show #!3.1,4 surfaces
> hide #!3.1,4 surfaces
> hide #!3.4 models
> show #!3.3 models
> show #!3.1,3 surfaces
> hide #!3.3 models
> show #!3.8 models
> hide #!3.8 models
> show #!3.21 models
> hide #!3.21 models
> show #!3.2 models
> show #!3.11 models
> hide #!3.11 models
> show #!3.17 models
> hide #!3.17 models
> show #!3.17 models
> hide #!3.17 models
> hide #!3.2 models
> hide #!3.1 models
> show #!3.3 models
> show #!3.1 models
> show #!3.4 models
> hide #!3.3 models
> hide #!3.1,4 surfaces
> cartoon style #3.1,4#!3 modeHelix tube sides 20
> cartoon style (#3.1,4#!3 & coil) xsection oval
> cartoon style #3.1,4#!3 xsection barbell modeHelix default
> lighting intensity 0.45 ambientIntensity 0.14 fillIntensity 1 depthCue true
> shadows true multiShadow 64
> select add #3.1
2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected
> ui tool show "Color Actions"
> color sel pink
> select clear
> show #!3.1,4 atoms
> color #3.1,4#!3 byhetero
> ui mousemode right distance
> distance #3.4/Ad:135@OE1 #3.1/Aa:455@NH1
Distance between chains_filament16_real_space_refined.pdb Ad #3.4/Ad GLU 135
OE1 and chains_filament16_real_space_refined.pdb Aa #3.1/Aa ARG 455 NH1:
5.036Å
> hide #!3.1,4 atoms
> select #3.4/Ad:135
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:455
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> ui tool show "Color Actions"
> color sel lime
> select #3.4/Ad:126
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:413
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> distance #3.1/Aa:413@NZ #3.4/Ad:126@OG1
Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa LYS 413
NZ and chains_filament16_real_space_refined.pdb Ad #3.4/Ad THR 126 OG1: 3.203Å
> select clear
> hide #5.1 models
> save "/Users/nezakoritnik/Desktop/INTERFACE 1/od-cd.png" width 3000 height
> 2435 supersample 3 transparentBackground true
> save "/Users/nezakoritnik/Desktop/INTERFACE 1/od-cd.cxs"
——— End of log from Tue Jan 28 10:12:17 2025 ———
opened ChimeraX session
> save "/Users/nezakoritnik/Desktop/INTERFACE 1/od-cd.png" width 3000 height
> 2435 supersample 3 transparentBackground true
> hide #!3.1,4 atoms
> ui tool show "Show Sequence Viewer"
> sequence chain #3.1/Aa
Alignment identifier is 3.1/Aa
> select #3.1/Aa:457
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3.1/Aa:377-457
635 atoms, 649 bonds, 81 residues, 1 model selected
> select #3.1/Aa:273
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3.1/Aa:273-457
1181 atoms, 1205 bonds, 1 pseudobond, 151 residues, 2 models selected
> select #3.1/Aa:253
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.1/Aa:253-457
1339 atoms, 1363 bonds, 1 pseudobond, 171 residues, 2 models selected
> select #3.1/Aa:167
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.1/Aa:167-457
1528 atoms, 1553 bonds, 2 pseudobonds, 195 residues, 2 models selected
> select #3.1/Aa:175
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3.1/Aa:175-457
1460 atoms, 1485 bonds, 2 pseudobonds, 187 residues, 2 models selected
> cartoon hide (#!3.1 & sel)
> select #3.1/Aa:101
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3.1/Aa:101-140
333 atoms, 341 bonds, 40 residues, 1 model selected
> select #3.1/Aa:145
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3.1/Aa:101-145
367 atoms, 375 bonds, 45 residues, 1 model selected
> cartoon hide (#!3.1 & sel)
> ui tool show "Show Sequence Viewer"
> sequence chain #3.4/Ad
Alignment identifier is 3.4/Ad
> select #3.4/Ad:457
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3.4/Ad:253-457
1339 atoms, 1363 bonds, 1 pseudobond, 171 residues, 2 models selected
> select #3.4/Ad:167
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.4/Ad:167-457
1528 atoms, 1553 bonds, 2 pseudobonds, 195 residues, 2 models selected
> select #3.4/Ad:148
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.4/Ad:148-457
1677 atoms, 1705 bonds, 2 pseudobonds, 214 residues, 2 models selected
> hide sel cartoons
> select #3.1/Aa:166
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.4/Ad:130
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> distance #3.1/Aa:166@NH1 #3.4/Ad:130@OH
Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa ARG 166
NH1 and chains_filament16_real_space_refined.pdb Ad #3.4/Ad TYR 130 OH: 3.848Å
> select clear
> select #3.1/Aa:163
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.4/Ad:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:169
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> distance #3.1/Aa:169@OG1 #3.4/Ad:130@OH
Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa THR 169
OG1 and chains_filament16_real_space_refined.pdb Ad #3.4/Ad TYR 130 OH: 2.497Å
> select #3.1/Aa:170
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #3.1/Aa:171
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.4/Ad:127
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> distance #3.1/Aa:171@OD1 #3.4/Ad:127@NE2
Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa ASN 171
OD1 and chains_filament16_real_space_refined.pdb Ad #3.4/Ad GLN 127 NE2:
6.116Å
> hide sel atoms
> select #3.1/Aa:171
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/Aa:159
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.4/Ad:133
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.4/Ad:118
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.4/Ad:114
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:162
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:155
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.4/Ad:141
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3.4/Ad:140
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.1/Aa:158
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.4/Ad:137
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #3.4/Ad:140
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:154
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.4/Ad:137
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.4/Ad:137
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.4/Ad:111
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #3.4/Ad:136
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:161
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.4/Ad:136@CA
1 atom, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #3.4/Ad:136
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/Aa:162
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3.1/Aa:161
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.1/Aa:165
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.4/Ad:129
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.4/Ad:137
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.4/Ad:137
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.4/Ad:136
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.4/Ad:137
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #3.1/Aa:151
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> save "/Users/nezakoritnik/Desktop/INTERFACE 1/od-od.cxs"
> ui tool show "Side View"
> select #3.4/Ad:109
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> distance #3.4/Ad:109@OD1 #3.1/Aa:163@NH1
Distance between chains_filament16_real_space_refined.pdb Ad #3.4/Ad ASN 109
OD1 and chains_filament16_real_space_refined.pdb Aa #3.1/Aa ARG 163 NH1:
14.827Å
> ~distance #3.4/Ad:109@OD1 #3.1/Aa:163@NH1
> distance #3.1/Aa:163@NH1 #3.4/Ad:117@OE1
Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa ARG 163
NH1 and chains_filament16_real_space_refined.pdb Ad #3.4/Ad GLU 117 OE1:
4.957Å
> distance #3.4/Ad:109@OD1 #3.1/Aa:155@OG
Distance between chains_filament16_real_space_refined.pdb Ad #3.4/Ad ASN 109
OD1 and chains_filament16_real_space_refined.pdb Aa #3.1/Aa SER 155 OG: 3.725Å
> turn y 180
[Repeated 18 time(s)]
> select #3.4/Ad:129
7 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> turn y 180
[Repeated 4 time(s)]
> select clear
> save "/Users/nezakoritnik/Desktop/INTERFACE 1/od-od1.png" width 3000 height
> 2435 supersample 3 transparentBackground true
> turn y 180
> save "/Users/nezakoritnik/Desktop/INTERFACE 1/od-od1.png" width 3000 height
> 2435 supersample 3 transparentBackground true
> undo
[Repeated 1 time(s)]
> select clear
> color sel lime
> select clear
> save "/Users/nezakoritnik/Desktop/INTERFACE 1/od-od1.png" width 3000 height
> 2435 supersample 3 transparentBackground true
> turn y 180
> save "/Users/nezakoritnik/Desktop/INTERFACE 1/od-od2.png" width 3000 height
> 2435 supersample 3 transparentBackground true
> save "/Users/nezakoritnik/Desktop/INTERFACE 1/od-od.cxs"
> hide #!5 models
> select #3.4/Ad:101
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3.4/Ad
2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected
> show sel cartoons
> hide sel atoms
> select #3.1/Aa:456-457
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #3.1/Aa
2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected
> show sel cartoons
> hide sel atoms
> select clear
> save "/Users/nezakoritnik/Desktop/INTERFACE 1/celoten.cxs"
> save "/Users/nezakoritnik/Desktop/INTERFACE 1/celoten.png" width 3000 height
> 2435 supersample 3
> show #!3.3 models
> hide #!3.4 models
> hide #!3.1,3 surfaces
> select add #3.3
2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected
> ui tool show "Color Actions"
> color sel aquamarine
> color sel medium aquamarine
> color sel mint cream
> color sel pale turquoise
> show #!3.4 models
> ui tool show "Color Actions"
> color #3.3 #a4c4b3ff
> color #3.3 #dbfdefff
> color #3.3 #cdf4e1ff
> hide #!3.4 models
> select clear
> save "/Users/nezakoritnik/Desktop/INTERFACE 2/celoten.png" width 3000 height
> 2435 supersample 3
> show #!3.4 models
> hide #!3.3 models
> select clear
> select #3.4/Ad:450
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:126
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:127
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> select clear
> select #3.1/Aa:128
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.4/Ad:453
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:164
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:157
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:132
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!3.3 models
> hide #!3.4 models
> select #3.1/Aa:457
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3.1/Aa:169-457
1509 atoms, 1534 bonds, 2 pseudobonds, 193 residues, 2 models selected
> hide sel cartoons
> ui tool show "Show Sequence Viewer"
> sequence chain #3.3/Ac
Alignment identifier is 3.3/Ac
> select #3.3/Ac:101
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3.3/Ac:101-183
666 atoms, 678 bonds, 83 residues, 1 model selected
> hide sel cartoons
[Repeated 1 time(s)]
> hide sel atoms
[Repeated 1 time(s)]
> select clear
> hide #!3.1,3 atoms
> select #3.1/Aa:113
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #3.1/Aa:106
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.3/Ac:362
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> color #3.1,3#!3 byhetero
> distance #3.1/Aa:106@NH1 #3.3/Ac:362@OD2
Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa ARG 106
NH1 and chains_filament16_real_space_refined.pdb Ac #3.3/Ac ASP 362 OD2:
2.728Å
> distance #3.3/Ac:362@OD2 #3.1/Aa:106@NH1
Distance already exists; modify distance properties with 'distance style'
> show #!5 models
> color sel lime
> select #3.1/Aa:145
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
[Repeated 1 time(s)]
> show sel atoms
> select #3.3/Ac:357
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.3/Ac:358
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.3/Ac:359
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> select #3.3/Ac:360
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select clear
> select #3.3/Ac:358
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/Aa:145
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.3/Ac:359
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.3/Ac:357
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/Aa:115
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.3/Ac:389
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> ui mousemode right distance
> distance #3.1/Aa:115@OH #3.3/Ac:389@OG
Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa TYR 115
OH and chains_filament16_real_space_refined.pdb Ac #3.3/Ac SER 389 OG: 2.696Å
> select #3.1/Aa:116
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.3/Ac:374
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> distance #3.1/Aa:116@NH1 #3.3/Ac:374@OD2
Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa ARG 116
NH1 and chains_filament16_real_space_refined.pdb Ac #3.3/Ac ASP 374 OD2:
3.301Å
> color sel lime
> select #3.1/Aa:120
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.3/Ac:445
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> distance #3.1/Aa:120@NZ #3.3/Ac:445@OD1
Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa LYS 120
NZ and chains_filament16_real_space_refined.pdb Ac #3.3/Ac ASN 445 OD1: 3.904Å
> select #3.1/Aa:138
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.3/Ac:437
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:135
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.3/Ac:440
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.3/Ac:437
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3.3/Ac:437
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/Aa:135
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.3/Ac:393
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3.1/Aa:142
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.3/Ac:394
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:142
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/Aa:141
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.3/Ac:390
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:142
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> select #3.1/Aa:119
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.3/Ac:386
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.3/Ac:390
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.3/Ac:440
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.3/Ac:443
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> hide sel atoms
> cartoon style (#!3.3 & sel) modeHelix tube sides 20
[Repeated 1 time(s)]
> cartoon style (#!3.3 & sel & coil) xsection oval
> cartoon style (#!3.3 & sel) xsection barbell modeHelix default
> select clear
> select #3.1/Aa:138
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> turn y 180
[Repeated 1 time(s)]
> save "/Users/nezakoritnik/Desktop/INTERFACE 2/interface1.png" width 3000
> height 2435 supersample 3 transparentBackground true
> turn y 180
> save "/Users/nezakoritnik/Desktop/INTERFACE 2/interface2.png" width 3000
> height 2435 supersample 3 transparentBackground true
> save "/Users/nezakoritnik/Desktop/INTERFACE 2/interface.cxs"
——— End of log from Tue Jan 28 14:16:05 2025 ———
opened ChimeraX session
> close #4
> show #!3.2 models
> ui tool show "Side View"
> hide #!3.1 models
> show #!3.1 models
> hide #!3.2 models
> show #!3.5 models
> hide #!3.5 models
> show #!3.5 models
> hide #!3.5 models
> show #!3.7 models
> hide #!3.7 models
> show #!3.9 models
> show #!3.8 models
> hide #!3.8 models
> hide #!3.9 models
> show #!3.10 models
> hide #!3.10 models
> show #!3.11 models
> show #!3.12 models
> hide #!3.11 models
> hide #!3.12 models
> show #!3.14 models
> hide #!3.14 models
> show #!3.15 models
> hide #!3.15 models
> show #!3.16 models
> hide #!3.16 models
> show #!3.17 models
> hide #!3.17 models
> show #!3.20 models
> hide #!3.20 models
> show #!3.20 models
> hide #!3.20 models
> show #!3.20 models
> hide #!3.20 models
> show #!3.20 models
> hide #!3.20 models
> show #!3.21 models
> hide #!3.21 models
> show #!3.21 models
> hide #!3.21 models
> show #!3.22 models
> hide #!3.22 models
> show #!3.21 models
> hide #!3.21 models
> select #3.3/Ac:407-457
409 atoms, 416 bonds, 51 residues, 1 model selected
> select #3.3/Ac
2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected
> show sel cartoons
> select #3.1/Aa:457
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3.1/Aa
2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected
> show sel cartoons
> show #!3.21 models
> hide sel surfaces
> select clear
> hide #!3.1,3,21 surfaces
> color #3.21 #e0fef3ff
> color #3.21 #c8e7d8ff
> cartoon style (#3.1,3,21#!3,5 & coil) xsection oval
> cartoon style #3.1,3,21#!3,5 xsection barbell modeHelix default
> hide #!3.3 models
> hide #!3.1,21 atoms
> save "/Users/nezakoritnik/Desktop/INTERFACE 3/celotna.png" width 3000 height
> 2435 supersample 3 transparentBackground true
> save "/Users/nezakoritnik/Desktop/INTERFACE 3/celotna.cxs"
> select #3.1/Aa:265
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:261
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:258
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.21/Au:254
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:254
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.21/Au:258
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.21/Au:261
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.21/Au:265
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:457
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3.1/Aa:298-457
994 atoms, 1015 bonds, 1 pseudobond, 126 residues, 2 models selected
> cartoon hide (#!3.1 & sel)
> select #3.1/Aa:297
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.1/Aa:270-297
213 atoms, 215 bonds, 28 residues, 1 model selected
> select #3.1/Aa:272
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3.1/Aa:272-297
196 atoms, 198 bonds, 26 residues, 1 model selected
> surface hidePatches (#!3.1 & sel)
> ui tool show "Show Sequence Viewer"
> sequence chain #3.21/Au
Alignment identifier is 3.21/Au
> select #3.21/Au:449-457
77 atoms, 78 bonds, 9 residues, 1 model selected
> select #3.21/Au:272-457
1190 atoms, 1214 bonds, 1 pseudobond, 152 residues, 2 models selected
> cartoon hide (#!3.21 & sel)
> select #3.21/Au:189
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #3.21/Au:101-189
709 atoms, 722 bonds, 89 residues, 1 model selected
> cartoon hide (#!3.21 & sel)
> select #3.1/Aa:189
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #3.1/Aa:101-189
709 atoms, 722 bonds, 89 residues, 1 model selected
> cartoon hide (#!3.1 & sel)
> select #3.1/Aa:281-282
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #3.1/Aa:281-297
132 atoms, 134 bonds, 17 residues, 1 model selected
> select #3.1/Aa:272
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3.1/Aa:272-297
196 atoms, 198 bonds, 26 residues, 1 model selected
> cartoon hide (#!3.1 & sel)
> select #3.1/Aa:266
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3.1/Aa:266-271
45 atoms, 44 bonds, 6 residues, 1 model selected
> hide (#!3.1 & sel) target a
> select #3.21/Au:266
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3.21/Au:266-275
75 atoms, 74 bonds, 10 residues, 1 model selected
> select #3.21/Au:267-268
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #3.21/Au:267-284
128 atoms, 127 bonds, 18 residues, 1 model selected
> cartoon hide (#!3.21 & sel)
> select #3.1/Aa:267
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3.1/Aa:267-278
87 atoms, 86 bonds, 12 residues, 1 model selected
> cartoon hide (#!3.1 & sel)
> save "/Users/nezakoritnik/Desktop/INTERFACE 3/interface.cxs"
> save "/Users/nezakoritnik/Desktop/INTERFACE 3/interface.png" width 3000
> height 2435 supersample 3 transparentBackground true
[Repeated 1 time(s)]
> undo
> surface hidePatches (#!3.1 & sel)
> select #3.1/Aa:457
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3.1/Aa
2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected
> show sel cartoons
> select #3.21/Au:457
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3.21/Au
2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected
> show sel cartoons
> ui tool show "Model Panel"
> show #!3.2 models
> show sel surfaces
> select clear
> show #!3.1-2,21 surfaces
> hide #!3.1-2,21 surfaces
> ui tool show "Show Sequence Viewer"
> sequence chain #3.2/Ab
Alignment identifier is 3.2/Ab
> select #3.2/Ab:105
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3.2/Ab:105-386
1462 atoms, 1484 bonds, 2 pseudobonds, 186 residues, 2 models selected
> select #3.2/Ab:386-387
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #3.2/Ab:101-387
1507 atoms, 1532 bonds, 2 pseudobonds, 191 residues, 2 models selected
> select #3.2/Ab:101
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3.2/Ab:101
12 atoms, 12 bonds, 1 residue, 1 model selected
> color #3.2 #daf6e9ff
> color #3.2 #d4efe3ff
> select add #3.2
2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 5 models selected
> select subtract #3.2
1 model selected
> hide #!3.21 models
> hide #!3.1-2 atoms
> select #3.1/Aa:173
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.2/Ab:285
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> hide #!3.1-2 atoms
> cartoon style (#3.1-2#!3,5 & coil) xsection oval
> cartoon style #3.1-2#!3,5 xsection barbell modeHelix default
> ui tool show "Side View"
> save "/Users/nezakoritnik/Desktop/INTERFACE 4/celotna.png" width 3000 height
> 2435 supersample 3 transparentBackground true
> save "/Users/nezakoritnik/Desktop/INTERFACE 4/celotna.cxs"
> select #3.1/Aa:173
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.2/Ab:284
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> show sel atoms
> select clear
> color #3.1-2#!3,5 byhetero
> select #3.2/Ab:285
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:163
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.2/Ab:120
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3.2/Ab:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> distance #3.2/Ab:117@OE2 #3.1/Aa:163@NH1
Distance between chains_filament16_real_space_refined.pdb Ab #3.2/Ab GLU 117
OE2 and chains_filament16_real_space_refined.pdb Aa #3.1/Aa ARG 163 NH1:
5.233Å
> show #5.1 models
> hide #5.1 models
> ui tool show "Color Actions"
> color sel lime
> select #3.1/Aa:173@NZ
1 atom, 1 residue, 1 model selected
> select clear
> select #3.1/Aa:173@NZ
1 atom, 1 residue, 1 model selected
> select #3.2/Ab:284@OD2
1 atom, 1 residue, 1 model selected
> select #3.1/Aa:173@NZ
1 atom, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #3.2/Ab:284@OD2
1 atom, 1 residue, 1 model selected
> select #3.1/Aa:173@NZ
1 atom, 1 residue, 1 model selected
> select #3.2/Ab:284@OD2
1 atom, 1 residue, 1 model selected
> select add #3.1/Aa:173@NZ
2 atoms, 2 residues, 3 models selected
> select subtract #3.2/Ab:284@OD2
1 atom, 1 residue, 3 models selected
> select #3.1/Aa:173@NZ
1 atom, 1 residue, 1 model selected
Drag select of 1 atoms
> select #3.1/Aa:173@NZ
1 atom, 1 residue, 1 model selected
> select #3.2/Ab:284@OD2
1 atom, 1 residue, 1 model selected
> select #3.1/Aa:173@NZ
1 atom, 1 residue, 1 model selected
> select clear
> select #3.1/Aa:173@NZ
1 atom, 1 residue, 1 model selected
> select #3.2/Ab:284@OD2
1 atom, 1 residue, 1 model selected
> select clear
> select #3.1/Aa:173@NZ
1 atom, 1 residue, 1 model selected
> distance #3.1/Aa:173@NZ #3.2/Ab:284@OD2
Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa LYS 173
NZ and chains_filament16_real_space_refined.pdb Ab #3.2/Ab ASP 284 OD2: 3.248Å
> distance #3.1/Aa:173@NZ #3.2/Ab:285@OD1
Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa LYS 173
NZ and chains_filament16_real_space_refined.pdb Ab #3.2/Ab ASN 285 OD1: 3.099Å
> color sel lime
> select #3.2/Ab:187
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> show sel atoms
> select #3.1/Aa:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> ui mousemode right distance
> distance #3.1/Aa:268@OE2 #3.2/Ab:187@NZ
Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa GLU 268
OE2 and chains_filament16_real_space_refined.pdb Ab #3.2/Ab LYS 187 NZ: 5.543Å
> select clear
> color sel lime
> select #3.2/Ab:286
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:276
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:275
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:274
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:273
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:277
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:273
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3.1/Aa:272
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:271
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:272
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3.2/Ab:287
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.2/Ab:288
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.2/Ab:289
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
Drag select of 1 residues
> select #3.2/Ab:290
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #3.2/Ab:289
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #3.2/Ab:288
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #3.2/Ab:287
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.2/Ab:286@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #3.2/Ab:286
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/Aa:277
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/Aa:276
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/Aa:275
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/Aa:274
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> hide sel atoms
> select #3.2/Ab:437
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:271
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/Aa:272
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #3.1/Aa:411
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/Aa:273
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/Aa:271
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.2/Ab:288
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #3.2/Ab:289
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #3.2/Ab:286
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> show sel atoms
> select #3.2/Ab:289
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.2/Ab:288
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.2/Ab:287
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #3.2/Ab:288
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #3.2/Ab:289
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.2/Ab:286
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> distance #3.2/Ab:437@NH2 #3.1/Aa:411@OD2
Distance between chains_filament16_real_space_refined.pdb Ab #3.2/Ab ARG 437
NH2 and chains_filament16_real_space_refined.pdb Aa #3.1/Aa ASP 411 OD2:
7.180Å
> show #5.1 models
> hide #5.1 models
> select clear
[Repeated 2 time(s)]
> color sel lime
> select #3.1/Aa:277
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #3.1/Aa:413
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> show sel atoms
> hide sel atoms
> select #3.1/Aa:271
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> save "/Users/nezakoritnik/Desktop/INTERFACE 4/interakcijska površina.cxs"
——— End of log from Wed Jan 29 07:29:35 2025 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir10,1
Model Number: Z128000N6ZE/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 8419.80.7
OS Loader Version: 8419.80.7
Software:
System Software Overview:
System Version: macOS 13.2 (22D49)
Kernel Version: Darwin 22.3.0
Time since boot: 16 days, 19 hours, 49 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
HP E243i:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
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: 1.18.1
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
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: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 9 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 9 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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