![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 19 months ago
Closed 19 months ago
#14805 closed defect (nonchimerax)
Graphics crash, macOS 13.4, Intel Iris Plus Graphics 640
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-13.4-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Current thread 0x00007ff84b76b640 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 248 in swap_buffers
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 556 in swap_buffers
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 202 in draw
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 84 in draw_new_frame
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.mlp._mlp, chimerax.atom_search.ast, chimerax.chem_group._chem_group, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._isolve._iterative, 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.linalg._flinalg, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, 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._minpack2, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, numpy.linalg.lapack_lite, 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.__nnls, 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, PIL._webp (total: 118)
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"procLaunch" : "2024-03-14 12:25:52.3174 +0000",
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===== Log before crash start =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/sarah/Documents/Work/PKS13/PKS13-dimer-fit172-coot.pdb format
> pdb
Chain information for PKS13-dimer-fit172-coot.pdb #1
---
Chain | Description
A | No description available
B | No description available
> set bgColor white
> open "/Users/sarah/Documents/Work/PKS13/3i8p FabF platensimycin.pdb"
3i8p FabF platensimycin.pdb title:
Crystal structure of E. Coli fabf(C163A) In complex with platensimycin A1
[more info...]
Chain information for 3i8p FabF platensimycin.pdb #2
---
Chain | Description | UniProt
A | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | FABF_ECOLI -14-412
Non-standard residues in 3i8p FabF platensimycin.pdb #2
---
840 — platensimycin A1
(2,4-dihydroxy-3-({3-[(1AR,2R,3R,3AS,7S,7AS,7BR)-3-hydroxy-2,7-dimethyl-6-oxo-2,3,7,7A-tetrahydro-6H-2,7B-epoxy-1A,3A-me
thanocyclopropa[A]naphthalen-7(1H)-yl]propanoyl}amino)benzoic acid)
> ui tool show Matchmaker
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PKS13-dimer-fit172-coot.pdb, chain B (#1) with 3i8p FabF
platensimycin.pdb, chain A (#2), sequence alignment score = 654.7
RMSD between 260 pruned atom pairs is 1.117 angstroms; (across all 400 pairs:
3.670)
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PKS13-dimer-fit172-coot.pdb, chain B (#1) with 3i8p FabF
platensimycin.pdb, chain A (#2), sequence alignment score = 654.7
RMSD between 260 pruned atom pairs is 1.117 angstroms; (across all 400 pairs:
3.670)
> select ::name="840"
33 atoms, 38 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A
6900 atoms, 7047 bonds, 1 pseudobond, 922 residues, 2 models selected
> hide sel cartoons
> ui mousemode right select
Drag select of 447 residues, 1 pseudobonds
Drag select of 421 residues, 1 pseudobonds
> hide sel cartoons
Drag select of 45 residues
> hide sel cartoons
Drag select of 39 residues
> ui mousemode right zoom
> ui windowfill toggle
> ui mousemode right "translate selected models"
> view matrix models
> #1,1,0,0,7.0047,0,1,0,-8.1788,0,0,1,-19.486,#2,-0.37428,-0.23973,0.89579,173.81,0.25984,0.9002,0.34948,134.91,-0.89017,0.36356,-0.27464,149.74
> ui windowfill toggle
> view matrix models
> #1,1,0,0,13.691,0,1,0,-2.5047,0,0,1,-18.599,#2,-0.37428,-0.23973,0.89579,180.5,0.25984,0.9002,0.34948,140.59,-0.89017,0.36356,-0.27464,150.63
> ui mousemode right zoom
> ui mousemode right select
> select #1/B:530
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/B:528
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> ui tool show "Color Actions"
> open "/Users/sarah/Documents/Work/PKS13/2gfy FabF dodecanoic acid.pdb"
2gfy FabF dodecanoic acid.pdb title:
Structure of E. Coli fabf(K335A) mutant with covalently linked dodecanoic acid
[more info...]
Chain information for 2gfy FabF dodecanoic acid.pdb #3
---
Chain | Description | UniProt
A | 3-oxoacyl-[ACYL-carrier-protein] synthase II; β-ketoacyl- ACP synthase II;
KAS II; FABF | FABF_ECOLI 1-412
Non-standard residues in 2gfy FabF dodecanoic acid.pdb #3
---
DAO — lauric acid
> color #2 #f4f1edff
> undo
> color #3 #89cdebff
> color #1 #d6c1d3ff
> undo
> color #2 #d1b58cff
> color #1 #8bccebff
> close #3
> select add #1
13804 atoms, 14099 bonds, 2 pseudobonds, 1845 residues, 2 models selected
> select add #2
17379 atoms, 17193 bonds, 2 pseudobonds, 2795 residues, 3 models selected
> color (#2#!1 & sel) byhetero
> select ::name="840"
33 atoms, 38 bonds, 1 residue, 1 model selected
[deleted to fit within ticket limits]
Start residue of secondary structure not found: SHEET 9 9 1 ALA A 289 GLN A
298 0
50 messages similar to the above omitted
Pks13 cerulin platensimycin.pdb title:
Crystal structure of [KS3][AT3] didomain from module 3 of 6- deoxyerthronolide
B synthase [more info...]
Chain information for Pks13 cerulin platensimycin.pdb
---
Chain | Description | UniProt
1.1/A 1.1/B | 6 deoxyerythronolide B synthase | A4F7P0_SACEN 27-922
1.2/A | 6 deoxyerythronolide B synthase | A4F7P0_SACEN 27-922
1.3/A | 6 deoxyerythronolide B synthase | A4F7P0_SACEN 27-922
1.2/B | 6 deoxyerythronolide B synthase | A4F7P0_SACEN 27-922
> close #1
> open "/Users/sarah/Documents/Work/PKS13/6c4q ACP1.pdb"
6c4q ACP1.pdb title:
1.16 angstrom resolution crystal structure of acyl carrier protein domain
(residues 1-100) of polyketide synthase PKS13 from mycobacterium tuberculosis
[more info...]
Chain information for 6c4q ACP1.pdb #1
---
Chain | Description | UniProt
A | polyketide synthase PKS13 | I6X8D2_MYCTU 1-100
Non-standard residues in 6c4q ACP1.pdb #1
---
EDO — 1,2-ethanediol (ethylene glycol)
MPD — (4S)-2-methyl-2,4-pentanediol
> select /A:201@C2
1 atom, 1 residue, 1 model selected
> select ::name="MPD"
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select ::name="EDO"
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel atoms
> select ::name="HOH"
124 atoms, 124 residues, 1 model selected
> hide sel atoms
> select
770 atoms, 654 bonds, 211 residues, 1 model selected
> hide sel atoms
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select /A:55
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:55
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select
770 atoms, 654 bonds, 211 residues, 1 model selected
> color sel orange
> ui tool show "Color Actions"
> color sel dark orange target acspfl
> color sel byhetero target acspfl
> select clear
> save "/Users/sarah/Documents/Work/PKS13/DH AlphaFold/ACP1.tif" width 5000
> height 2698 supersample 3 transparentBackground true
> open "/Users/sarah/Documents/Work/PKS13/6c4v ACP3.pdb"
6c4v ACP3.pdb title:
1.9 angstrom resolution crystal structure of acyl carrier protein domain
(residues 1350-1461) of polyketide synthase PKS13 from mycobacterium
tuberculosis [more info...]
Chain information for 6c4v ACP3.pdb #2
---
Chain | Description | UniProt
A | polyketide synthase PKS13 | I6X8D2_MYCTU 1349-1461
Non-standard residues in 6c4v ACP3.pdb #2
---
ZN — zinc ion
> close #1
Drag select of 10 residues
> ui mousemode right translate
> select clear
> select
648 atoms, 619 bonds, 5 pseudobonds, 119 residues, 2 models selected
> hide sel atoms
> color (#!2 & sel) orange
> select clear
> open "/Users/sarah/Documents/Work/PKS13/6c4q ACP1.pdb"
6c4q ACP1.pdb title:
1.16 angstrom resolution crystal structure of acyl carrier protein domain
(residues 1-100) of polyketide synthase PKS13 from mycobacterium tuberculosis
[more info...]
Chain information for 6c4q ACP1.pdb #1
---
Chain | Description | UniProt
A | polyketide synthase PKS13 | I6X8D2_MYCTU 1-100
Non-standard residues in 6c4q ACP1.pdb #1
---
EDO — 1,2-ethanediol (ethylene glycol)
MPD — (4S)-2-methyl-2,4-pentanediol
> ui tool show Matchmaker
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6c4q ACP1.pdb, chain A (#1) with 6c4v ACP3.pdb, chain A (#2),
sequence alignment score = 98.3
RMSD between 29 pruned atom pairs is 1.050 angstroms; (across all 75 pairs:
7.068)
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6c4q ACP1.pdb, chain A (#1) with 6c4v ACP3.pdb, chain A (#2),
sequence alignment score = 98.3
RMSD between 29 pruned atom pairs is 1.050 angstroms; (across all 75 pairs:
7.068)
> hide #1 models
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> save /Users/sarah/Documents/Work/PKS13/ACP3.tif width 5000 height 2698
> supersample 3 transparentBackground true
> open "/Users/sarah/Documents/Work/PKS13/5v40 TE.pdb"
5v40 TE.pdb title:
Crystal structure of MTB PKS13 thioesterase domain In complex with inhibitor
TAM6 [more info...]
Chain information for 5v40 TE.pdb #3
---
Chain | Description
A B | polyketide synthase PKS13 (termination polyketide synthase)
Non-standard residues in 5v40 TE.pdb #3
---
JS1 — ethyl
4-[(dimethylamino)methyl]-5-hydroxy-2-phenyl-1-benzofuran-3-carboxylate
> hide #!2 models
> hide #!3 atoms
> ui tool show "Color Actions"
> color deep sky blue target acspfl
> color byhetero target acspfl
> ui tool show "Color Actions"
> color cornflower blue target acspfl
> ui tool show "Color Actions"
> color sky blue target acspfl
> color #3 byhetero
> select #3/A
2367 atoms, 2193 bonds, 2 pseudobonds, 498 residues, 2 models selected
> hide sel cartoons
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A #3/B
Alignment identifier is 1
> select
> #3/A:1480-1490,1506-1523,1533-1549,1571-1590,1598-1603,1606-1620,1626-1645,1664-1676,1698-1702,1706-1727/B:1480-1490,1506-1523,1533-1549,1571-1589,1598-1603,1606-1621,1626-1645,1664-1676,1698-1702,1706-1726
2268 atoms, 2290 bonds, 293 residues, 1 model selected
> select #3/A-B:1533
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #3/A-B:1533
12 atoms, 10 bonds, 2 residues, 1 model selected
> show sel atoms
> ui mousemode right select
Drag select of 6 atoms, 5 bonds
> hide sel atoms
> ui mousemode right translate
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> save /Users/sarah/Documents/Work/PKS13/TE.tif width 5000 height 2698
> supersample 3 transparentBackground true
> ui tool show "Color Actions"
> color sel deep sky blue target acspfl
> select
6054 atoms, 5608 bonds, 8 pseudobonds, 1278 residues, 5 models selected
> ui tool show "Color Actions"
> color sel deep sky blue target acspfl
> color sel byhetero target acspfl
> select clear
> select
6054 atoms, 5608 bonds, 8 pseudobonds, 1278 residues, 5 models selected
> color (#!3 & sel) cyan
> select clear
> select
6054 atoms, 5608 bonds, 8 pseudobonds, 1278 residues, 5 models selected
> color (#!3 & sel) byhetero
> select clear
> select
6054 atoms, 5608 bonds, 8 pseudobonds, 1278 residues, 5 models selected
> ui tool show "Color Actions"
> color sel cornflower blue target acspfl
> ui tool show "Color Actions"
> color sel light sky blue target acspfl
> color (#!3 & sel) byhetero
> select clear
> save /Users/sarah/Documents/Work/PKS13/TE.tif width 5000 height 2698
> supersample 3 transparentBackground true
> close #1
> close
> open /Users/sarah/Documents/Work/PKS13/PKS13-dimer-fit172-coot.pdb
Chain information for PKS13-dimer-fit172-coot.pdb #1
---
Chain | Description
A | No description available
B | No description available
> open /Users/sarah/Documents/Work/PKS13/postprocess_masked_job165.mrc
Opened postprocess_masked_job165.mrc as #2, grid size 360,360,360, pixel 1.09,
shown at level 0.000365, step 2, values float32
> select add #2
2 models selected
> transparency #2.1 90
> ui tool show Matchmaker
> select clear
> ui mousemode right "contour level"
> volume #2 level -0.002336
> volume #2 level 0.01218
> volume #2 level 0.01447
> select /A
6900 atoms, 7047 bonds, 1 pseudobond, 922 residues, 2 models selected
> select /B
6904 atoms, 7052 bonds, 1 pseudobond, 923 residues, 2 models selected
> hide sel cartoons
> volume #2 step 1
> volume #2 level 0.02395
> select
13804 atoms, 14099 bonds, 2 pseudobonds, 1845 residues, 4 models selected
> volume #2 level 0.02065
> hide #!1 models
> show #!1 models
> volume #2 level 0.02272
> volume #2 step 2
> volume #2 step 16
> volume #2 level 0.01343
> volume #2 step 8
> volume #2 step 4
> volume #2 step 1
> volume #2 level 0.0225
> transparency (#!1 & sel) 80
> select clear
> transparency 60
> transparency 70
> volume #2 level 0.02126
> hide #!2 models
> ui mousemode right select
Drag select of 457 residues
> select add /A:1050
3443 atoms, 3 bonds, 458 residues, 1 model selected
> ui mousemode right zoom
> select up
3691 atoms, 3770 bonds, 488 residues, 1 model selected
> select up
6900 atoms, 7047 bonds, 922 residues, 1 model selected
> select up
13804 atoms, 14099 bonds, 1845 residues, 1 model selected
> select down
6900 atoms, 7047 bonds, 922 residues, 1 model selected
> select down
3691 atoms, 3770 bonds, 488 residues, 1 model selected
> select down
3443 atoms, 3 bonds, 458 residues, 1 model selected
> ui mousemode right select
> select add /A:1051
3450 atoms, 10 bonds, 459 residues, 1 model selected
> select add /A:668
3461 atoms, 20 bonds, 460 residues, 1 model selected
> select add /A:669
3469 atoms, 27 bonds, 461 residues, 1 model selected
> select add /A:1048
3474 atoms, 31 bonds, 462 residues, 1 model selected
> select add /A:1049
3480 atoms, 36 bonds, 463 residues, 1 model selected
Drag select of 2 residues
Drag select of 465 residues, 1 pseudobonds
> select subtract /A:370
3487 atoms, 1 pseudobond, 464 residues, 2 models selected
> color sel forest green
> ui tool show "Color Actions"
> color sel dark sea green target acspfl
> ui mousemode right select
Drag select of 79 residues
Drag select of 449 residues
> select add /A:368
3355 atoms, 10 bonds, 450 residues, 1 model selected
> select add /A:369
3363 atoms, 17 bonds, 451 residues, 1 model selected
> select add /A:1060
3370 atoms, 23 bonds, 452 residues, 1 model selected
> select subtract /A:1060
3363 atoms, 17 bonds, 451 residues, 1 model selected
> select add /A:1060
3370 atoms, 23 bonds, 452 residues, 1 model selected
> select add /A:549
3375 atoms, 27 bonds, 453 residues, 1 model selected
> select add /A:548
3382 atoms, 33 bonds, 454 residues, 1 model selected
> ui tool show "Color Actions"
> color sel khaki target acspfl
> select clear
> select add #2
2 models selected
> select subtract #2
Nothing selected
> show #!2 models
> volume #2 level 0.02332
> transparency 70
> transparency 80
> select clear
> ui mousemode right translate
> hide #!2 models
> ui mousemode right select
Drag select of 202 residues
Drag select of 450 residues
> select add /A:1063
3346 atoms, 8 bonds, 451 residues, 1 model selected
> select add /A:190
3357 atoms, 19 bonds, 452 residues, 1 model selected
> select add /A:189
3366 atoms, 27 bonds, 453 residues, 1 model selected
> select add /A:1060
3373 atoms, 33 bonds, 454 residues, 1 model selected
> select add /A:1061
3384 atoms, 43 bonds, 455 residues, 1 model selected
> select add /A:1062
3395 atoms, 54 bonds, 456 residues, 1 model selected
> ui tool show "Color Actions"
> color sel gold target acspfl
> color sel pale goldenrod target acspfl
> color sel wheat target acspfl
> ui tool show "Color Actions"
> color sel moccasin target acspfl
> color sel byhetero
> ui tool show "Color Actions"
> color sel khaki target acspfl
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain /B
Alignment identifier is 1/B
> select /B:287
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /B:287
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select /B:801
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /B:801
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> show sel atoms
> hide sel atoms
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select /A:801
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:801
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select
13804 atoms, 14099 bonds, 2 pseudobonds, 1845 residues, 4 models selected
> color (#!1 & sel) byhetero
> select clear
> show #!2 models
> hide #!2 models
> ui mousemode right select
> select clear
> select /B:287@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select /B:287@CB
1 atom, 1 residue, 1 model selected
> hide sel atoms
> ui tool show "Build Structure"
> select clear
Drag select of 4 atoms, 1 bonds
> hide sel atoms
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select /A:287
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:287
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> ui mousemode right translate
> show #!2 models
> transparency 90
> hide #!2 models
> show #!2 models
> select /A:287
6 atoms, 5 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 6 atom styles
> select /A:801
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:801
6 atoms, 5 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 6 atom styles
> select clear
> save "/Users/sarah/Documents/Work/PKS13/KS-AT density.tif" width 5000 height
> 3041 supersample 3 transparentBackground true
> transparency 80
> save "/Users/sarah/Documents/Work/PKS13/KS-AT density.tif" width 5000 height
> 3041 supersample 3 transparentBackground true
> surface style mesh
> surface style dot
> surface style solid
> transparency 70
> save "/Users/sarah/Documents/Work/PKS13/KS-AT density.tif" width 5000 height
> 3041 supersample 3 transparentBackground true
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> hide #!1 models
> hide #1.1 models
> show #1.1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #1.1 models
> hide #!1 models
> open /Users/sarah/Documents/Work/PKS13/PKS13-dimer-fit172-coot.pdb
Chain information for PKS13-dimer-fit172-coot.pdb #3
---
Chain | Description
A | No description available
B | No description available
> select #1/A
6900 atoms, 7047 bonds, 1 pseudobond, 922 residues, 2 models selected
> select add #1
13804 atoms, 14099 bonds, 2 pseudobonds, 1845 residues, 2 models selected
> select subtract #1.1
13804 atoms, 14099 bonds, 1845 residues, 1 model selected
> select add #1
13804 atoms, 14099 bonds, 2 pseudobonds, 1845 residues, 2 models selected
> select subtract #1
Nothing selected
> select #1/B
6904 atoms, 7052 bonds, 1 pseudobond, 923 residues, 2 models selected
> select #1/A#3/A
13800 atoms, 14094 bonds, 2 pseudobonds, 1844 residues, 4 models selected
> show #!1 models
> hide #!1 models
> select add #1
20704 atoms, 21146 bonds, 3 pseudobonds, 2767 residues, 4 models selected
> select subtract #1
6900 atoms, 7047 bonds, 1 pseudobond, 922 residues, 2 models selected
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> ui mousemode right select
Drag select of 132 residues
Drag select of 442 residues
> delete atoms sel
> delete bonds sel
Drag select of 2 residues, 2 pseudobonds
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> select #3/B:668
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
Drag select of 5 residues, 2 pseudobonds
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
No visible atoms or bonds selected
> save "/Users/sarah/Documents/Work/PKS13/Pks KS monomer.pdb" models #3
> displayedOnly true
> undo
Undo failed, probably because structures have been modified.
> undo
Undo failed, probably because structures have been modified.
> save "/Users/sarah/Documents/Work/PKS13/Pks KS monomer.pdb" models #3
> close #3
> open "/Users/sarah/Documents/Work/PKS13/Pks KS monomer.pdb"
Chain information for Pks KS monomer.pdb #3
---
Chain | Description
B | No description available
> close #3
> open /Users/sarah/Documents/Work/PKS13/PKS13-dimer-fit172-coot.pdb
Chain information for PKS13-dimer-fit172-coot.pdb #3
---
Chain | Description
A | No description available
B | No description available
> select #3/B
6904 atoms, 7052 bonds, 1 pseudobond, 923 residues, 2 models selected
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
Drag select of 421 residues
> delete atoms sel
> delete bonds sel
Drag select of 38 residues, 5 pseudobonds
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
Drag select of 1 pseudobonds
No visible atoms or bonds selected
> save "/Users/sarah/Documents/Work/PKS13/Pks AT monomer.pdb"
> save "/Users/sarah/Documents/Work/PKS13/Pks AT monomer.pdb" models #3
> close #3
> open "/Users/sarah/Documents/Work/PKS13/DH
> AlphaFold/test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb"
Chain information for
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb #3
---
Chain | Description
A B | No description available
> show #!2 models
> show #1.1 models
> hide #!1 models
> show #!1 models
> ui tool show Matchmaker
> matchmaker #3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PKS13-dimer-fit172-coot.pdb, chain B (#1) with
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb,
chain A (#3), sequence alignment score = 39
RMSD between 11 pruned atom pairs is 1.019 angstroms; (across all 70 pairs:
20.235)
> ui mousemode right "contour level"
> volume #2 level 0.01252
> volume #2 level 0.02219
> undo
> volume #2 level 0.02424
> select #3/B
507 atoms, 514 bonds, 70 residues, 1 model selected
> ui tool show "Fit in Map"
> fitmap #1 inMap #2
Fit molecule PKS13-dimer-fit172-coot.pdb (#1) to map
postprocess_masked_job165.mrc (#2) using 13804 atoms
average map value = 0.03415, steps = 48
shifted from previous position = 0.214
rotated from previous position = 0.836 degrees
atoms outside contour = 4670, contour level = 0.02424
Position of PKS13-dimer-fit172-coot.pdb (#1) relative to
postprocess_masked_job165.mrc (#2) coordinates:
Matrix rotation and translation
0.99997258 -0.00322857 -0.00666502 1.98278926
0.00331213 0.99991558 0.01256420 -3.12568373
0.00662389 -0.01258593 0.99989885 1.16227707
Axis -0.86167732 -0.45529594 0.22409329
Axis point 0.00000000 90.78017501 250.29115643
Rotation angle (degrees) 0.83618770
Shift along axis -0.02495495
> fitmap #1 inMap #2
Fit molecule PKS13-dimer-fit172-coot.pdb (#1) to map
postprocess_masked_job165.mrc (#2) using 13804 atoms
average map value = 0.03415, steps = 48
shifted from previous position = 0.0128
rotated from previous position = 0.0041 degrees
atoms outside contour = 4672, contour level = 0.02424
Position of PKS13-dimer-fit172-coot.pdb (#1) relative to
postprocess_masked_job165.mrc (#2) coordinates:
Matrix rotation and translation
0.99997229 -0.00329768 -0.00667349 2.01066478
0.00338123 0.99991556 0.01254716 -3.13541675
0.00663155 -0.01256938 0.99989901 1.15136920
Axis -0.86023996 -0.45569698 0.22875200
Axis point 0.00000000 90.25959304 251.85898478
Rotation angle (degrees) 0.83646603
Shift along axis -0.03747623
> fitmap #3 inMap #2
Fit molecule
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
to map postprocess_masked_job165.mrc (#2) using 1014 atoms
average map value = 0.01413, steps = 116
shifted from previous position = 2.56
rotated from previous position = 13.4 degrees
atoms outside contour = 704, contour level = 0.02424
Position of
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
relative to postprocess_masked_job165.mrc (#2) coordinates:
Matrix rotation and translation
0.17335867 0.46284400 -0.86932284 212.03673359
0.93647865 -0.35072460 0.00001832 205.42698059
-0.30488442 -0.81410545 -0.49424467 192.92183197
Axis -0.74142557 -0.51403618 0.43134085
Axis point 0.00000000 83.74248821 135.32701759
Rotation angle (degrees) 146.69978456
Shift along axis -179.59128960
> select #1/B#3/B
7411 atoms, 7566 bonds, 1 pseudobond, 993 residues, 3 models selected
> show sel cartoons
> fitmap #3 inMap #2
Fit molecule
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
to map postprocess_masked_job165.mrc (#2) using 1014 atoms
average map value = 0.01413, steps = 60
shifted from previous position = 0.0198
rotated from previous position = 0.052 degrees
atoms outside contour = 705, contour level = 0.02424
Position of
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
relative to postprocess_masked_job165.mrc (#2) coordinates:
Matrix rotation and translation
0.17294928 0.46357915 -0.86901261 212.04447882
0.93654857 -0.35053731 -0.00060573 205.43920519
-0.30490215 -0.81376776 -0.49478957 192.93588750
Axis -0.74133863 -0.51428481 0.43119390
Axis point 0.00000000 83.64204645 135.36234882
Rotation angle (degrees) 146.73982775
Shift along axis -179.65824826
> fitmap #3 inMap #2
Fit molecule
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
to map postprocess_masked_job165.mrc (#2) using 1014 atoms
average map value = 0.01413, steps = 48
shifted from previous position = 0.00122
rotated from previous position = 0.00974 degrees
atoms outside contour = 704, contour level = 0.02424
Position of
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
relative to postprocess_masked_job165.mrc (#2) coordinates:
Matrix rotation and translation
0.17303851 0.46346934 -0.86905342 212.04457365
0.93655335 -0.35052478 -0.00045762 205.43812608
-0.30483685 -0.81383570 -0.49471805 192.93643590
Axis -0.74135707 -0.51425770 0.43119452
Axis point 0.00000000 83.66142934 135.35419053
Rotation angle (degrees) 146.73077760
Shift along axis -179.65574903
> select #3/B
507 atoms, 514 bonds, 70 residues, 1 model selected
> volume #2 level 0.03638
> volume #2 level 0.007619
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.17304,0.46347,-0.86905,204.34,0.93655,-0.35052,-0.00045762,187.92,-0.30484,-0.81384,-0.49472,107.97
> fitmap #3 inMap #2
Fit molecule
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
to map postprocess_masked_job165.mrc (#2) using 1014 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 1014, contour level = 0.0076193
Position of
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
relative to postprocess_masked_job165.mrc (#2) coordinates:
Matrix rotation and translation
0.17303851 0.46346934 -0.86905342 204.33738185
0.93655335 -0.35052478 -0.00045762 187.92439116
-0.30483685 -0.81383570 -0.49471805 107.97316170
Axis -0.74135707 -0.51425770 0.43119452
Axis point 0.00000000 62.36151847 96.43121759
Rotation angle (degrees) 146.73077760
Shift along axis -201.57109281
> fitmap #3 inMap #2
Fit molecule
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
to map postprocess_masked_job165.mrc (#2) using 1014 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 1014, contour level = 0.0076193
Position of
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
relative to postprocess_masked_job165.mrc (#2) coordinates:
Matrix rotation and translation
0.17303851 0.46346934 -0.86905342 204.33738185
0.93655335 -0.35052478 -0.00045762 187.92439116
-0.30483685 -0.81383570 -0.49471805 107.97316170
Axis -0.74135707 -0.51425770 0.43119452
Axis point 0.00000000 62.36151847 96.43121759
Rotation angle (degrees) 146.73077760
Shift along axis -201.57109281
> select clear
> fitmap #3 inMap #2
Fit molecule
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
to map postprocess_masked_job165.mrc (#2) using 1014 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 1014, contour level = 0.0076193
Position of
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
relative to postprocess_masked_job165.mrc (#2) coordinates:
Matrix rotation and translation
0.17303851 0.46346934 -0.86905342 204.33738185
0.93655335 -0.35052478 -0.00045762 187.92439116
-0.30483685 -0.81383570 -0.49471805 107.97316170
Axis -0.74135707 -0.51425770 0.43119452
Axis point 0.00000000 62.36151847 96.43121759
Rotation angle (degrees) 146.73077760
Shift along axis -201.57109281
> fitmap #3 inMap #2
Fit molecule
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
to map postprocess_masked_job165.mrc (#2) using 1014 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 1014, contour level = 0.0076193
Position of
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
relative to postprocess_masked_job165.mrc (#2) coordinates:
Matrix rotation and translation
0.17303851 0.46346934 -0.86905342 204.33738185
0.93655335 -0.35052478 -0.00045762 187.92439116
-0.30483685 -0.81383570 -0.49471805 107.97316170
Axis -0.74135707 -0.51425770 0.43119452
Axis point 0.00000000 62.36151847 96.43121759
Rotation angle (degrees) 146.73077760
Shift along axis -201.57109281
> fitmap #3 inMap #2
Fit molecule
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
to map postprocess_masked_job165.mrc (#2) using 1014 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 1014, contour level = 0.0076193
Position of
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
relative to postprocess_masked_job165.mrc (#2) coordinates:
Matrix rotation and translation
0.17303851 0.46346934 -0.86905342 204.33738185
0.93655335 -0.35052478 -0.00045762 187.92439116
-0.30483685 -0.81383570 -0.49471805 107.97316170
Axis -0.74135707 -0.51425770 0.43119452
Axis point 0.00000000 62.36151847 96.43121759
Rotation angle (degrees) 146.73077760
Shift along axis -201.57109281
> fitmap #3 inMap #2
Fit molecule
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
to map postprocess_masked_job165.mrc (#2) using 1014 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 1014, contour level = 0.0076193
Position of
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
relative to postprocess_masked_job165.mrc (#2) coordinates:
Matrix rotation and translation
0.17303851 0.46346934 -0.86905342 204.33738185
0.93655335 -0.35052478 -0.00045762 187.92439116
-0.30483685 -0.81383570 -0.49471805 107.97316170
Axis -0.74135707 -0.51425770 0.43119452
Axis point 0.00000000 62.36151847 96.43121759
Rotation angle (degrees) 146.73077760
Shift along axis -201.57109281
> fitmap #3 inMap #2
Fit molecule
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
to map postprocess_masked_job165.mrc (#2) using 1014 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 1014, contour level = 0.0076193
Position of
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
relative to postprocess_masked_job165.mrc (#2) coordinates:
Matrix rotation and translation
0.17303851 0.46346934 -0.86905342 204.33738185
0.93655335 -0.35052478 -0.00045762 187.92439116
-0.30483685 -0.81383570 -0.49471805 107.97316170
Axis -0.74135707 -0.51425770 0.43119452
Axis point 0.00000000 62.36151847 96.43121759
Rotation angle (degrees) 146.73077760
Shift along axis -201.57109281
> volume #2 level 0.01713
> fitmap #3 inMap #2
Fit molecule
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
to map postprocess_masked_job165.mrc (#2) using 1014 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 1014, contour level = 0.017131
Position of
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
relative to postprocess_masked_job165.mrc (#2) coordinates:
Matrix rotation and translation
0.17303851 0.46346934 -0.86905342 204.33738185
0.93655335 -0.35052478 -0.00045762 187.92439116
-0.30483685 -0.81383570 -0.49471805 107.97316170
Axis -0.74135707 -0.51425770 0.43119452
Axis point 0.00000000 62.36151847 96.43121759
Rotation angle (degrees) 146.73077760
Shift along axis -201.57109281
> fitmap #3 inMap #2
Fit molecule
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
to map postprocess_masked_job165.mrc (#2) using 1014 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 1014, contour level = 0.017131
Position of
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
relative to postprocess_masked_job165.mrc (#2) coordinates:
Matrix rotation and translation
0.17303851 0.46346934 -0.86905342 204.33738185
0.93655335 -0.35052478 -0.00045762 187.92439116
-0.30483685 -0.81383570 -0.49471805 107.97316170
Axis -0.74135707 -0.51425770 0.43119452
Axis point 0.00000000 62.36151847 96.43121759
Rotation angle (degrees) 146.73077760
Shift along axis -201.57109281
> fitmap #3 inMap #2
Fit molecule
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
to map postprocess_masked_job165.mrc (#2) using 1014 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 1014, contour level = 0.017131
Position of
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
relative to postprocess_masked_job165.mrc (#2) coordinates:
Matrix rotation and translation
0.17303851 0.46346934 -0.86905342 204.33738185
0.93655335 -0.35052478 -0.00045762 187.92439116
-0.30483685 -0.81383570 -0.49471805 107.97316170
Axis -0.74135707 -0.51425770 0.43119452
Axis point 0.00000000 62.36151847 96.43121759
Rotation angle (degrees) 146.73077760
Shift along axis -201.57109281
> fitmap #1 inMap #2
Fit molecule PKS13-dimer-fit172-coot.pdb (#1) to map
postprocess_masked_job165.mrc (#2) using 13804 atoms
average map value = 0.03415, steps = 48
shifted from previous position = 0.00509
rotated from previous position = 0.0145 degrees
atoms outside contour = 2527, contour level = 0.017131
Position of PKS13-dimer-fit172-coot.pdb (#1) relative to
postprocess_masked_job165.mrc (#2) coordinates:
Matrix rotation and translation
0.99997332 -0.00307534 -0.00662644 1.95759746
0.00315906 0.99991486 0.01266099 -3.11009220
0.00658694 -0.01268159 0.99989789 1.18395957
Axis -0.86633963 -0.45170122 0.21312357
Axis point 0.00000000 92.01828225 247.64610935
Rotation angle (degrees) 0.83805147
Shift along axis -0.03878210
> fitmap #3 inMap #2
Fit molecule
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
to map postprocess_masked_job165.mrc (#2) using 1014 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 1014, contour level = 0.017131
Position of
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
relative to postprocess_masked_job165.mrc (#2) coordinates:
Matrix rotation and translation
0.17303851 0.46346934 -0.86905342 204.33738185
0.93655335 -0.35052478 -0.00045762 187.92439116
-0.30483685 -0.81383570 -0.49471805 107.97316170
Axis -0.74135707 -0.51425770 0.43119452
Axis point 0.00000000 62.36151847 96.43121759
Rotation angle (degrees) 146.73077760
Shift along axis -201.57109281
> fitmap #3 inMap #2
Fit molecule
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
to map postprocess_masked_job165.mrc (#2) using 1014 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 1014, contour level = 0.017131
Position of
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
relative to postprocess_masked_job165.mrc (#2) coordinates:
Matrix rotation and translation
0.17303851 0.46346934 -0.86905342 204.33738185
0.93655335 -0.35052478 -0.00045762 187.92439116
-0.30483685 -0.81383570 -0.49471805 107.97316170
Axis -0.74135707 -0.51425770 0.43119452
Axis point 0.00000000 62.36151847 96.43121759
Rotation angle (degrees) 146.73077760
Shift along axis -201.57109281
Average map value = 0 for 1014 atoms, 1014 outside contour
> volume #2 level 0.01781
> fitmap #3 inMap #2
Fit molecule
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
to map postprocess_masked_job165.mrc (#2) using 1014 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 1014, contour level = 0.01781
Position of
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
relative to postprocess_masked_job165.mrc (#2) coordinates:
Matrix rotation and translation
0.17303851 0.46346934 -0.86905342 204.33738185
0.93655335 -0.35052478 -0.00045762 187.92439116
-0.30483685 -0.81383570 -0.49471805 107.97316170
Axis -0.74135707 -0.51425770 0.43119452
Axis point 0.00000000 62.36151847 96.43121759
Rotation angle (degrees) 146.73077760
Shift along axis -201.57109281
> fitmap #3 inMap #2
Fit molecule
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
to map postprocess_masked_job165.mrc (#2) using 1014 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 1014, contour level = 0.01781
Position of
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
relative to postprocess_masked_job165.mrc (#2) coordinates:
Matrix rotation and translation
0.17303851 0.46346934 -0.86905342 204.33738185
0.93655335 -0.35052478 -0.00045762 187.92439116
-0.30483685 -0.81383570 -0.49471805 107.97316170
Axis -0.74135707 -0.51425770 0.43119452
Axis point 0.00000000 62.36151847 96.43121759
Rotation angle (degrees) 146.73077760
Shift along axis -201.57109281
> fitmap #3 inMap #2
Fit molecule
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
to map postprocess_masked_job165.mrc (#2) using 1014 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 1014, contour level = 0.01781
Position of
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
relative to postprocess_masked_job165.mrc (#2) coordinates:
Matrix rotation and translation
0.17303851 0.46346934 -0.86905342 204.33738185
0.93655335 -0.35052478 -0.00045762 187.92439116
-0.30483685 -0.81383570 -0.49471805 107.97316170
Axis -0.74135707 -0.51425770 0.43119452
Axis point 0.00000000 62.36151847 96.43121759
Rotation angle (degrees) 146.73077760
Shift along axis -201.57109281
> volume #2 level -0.0009864
> volume #2 level 0.003543
> volume #2 level -0.002119
> ui mousemode right select
> select add #3
1014 atoms, 1028 bonds, 140 residues, 1 model selected
> select add #1
14818 atoms, 15127 bonds, 2 pseudobonds, 1985 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.99997,-0.0030753,-0.0066264,12.12,0.0031591,0.99991,0.012661,-11.192,0.0065869,-0.012682,0.9999,21.171,#3,0.17304,0.46347,-0.86905,214.5,0.93655,-0.35052,-0.00045762,179.84,-0.30484,-0.81384,-0.49472,127.96
> view matrix models
> #1,0.99997,-0.0030753,-0.0066264,26.472,0.0031591,0.99991,0.012661,-45.459,0.0065869,-0.012682,0.9999,70.886,#3,0.17304,0.46347,-0.86905,228.85,0.93655,-0.35052,-0.00045762,145.58,-0.30484,-0.81384,-0.49472,177.67
> select add #2
14818 atoms, 15127 bonds, 2 pseudobonds, 1985 residues, 5 models selected
> volume #2 level 0.0008253
> volume #2 level -0.000307
> volume #2 level 0.0001459
> volume #2 level -0.0005212
> volume #2 style image
> volume #2 level 8.564e-06,0 level 0.0003632,0.8 level 0.1255,1
> volume #2 level 8.564e-06,0 level 0.005478,0.4765 level 0.1255,1
> volume #2 level 8.564e-06,0 level 0.00192,0.6324 level 0.1255,1
> volume #2 level 8.564e-06,0 level -0.009199,1 level 0.1255,1
> volume #2 level 8.564e-06,0 level -0.009199,1 level 0.09789,1
> volume #2 level -0.0002138,0.6471 level -0.009199,1 level 0.09789,1
> volume #2 level -0.0002138,0.6471 level -0.01898,0 level 0.09789,1
> volume #2 style surface
> volume #2 level -7.647e-05
> volume #2 level -0.0002988
> color #2 #c3c3c3ff models
> select subtract #3
13804 atoms, 14099 bonds, 2 pseudobonds, 1845 residues, 4 models selected
> select add #2
13804 atoms, 14099 bonds, 2 pseudobonds, 1845 residues, 5 models selected
> select subtract #1.1
13804 atoms, 14099 bonds, 1845 residues, 4 models selected
> select add #1
13804 atoms, 14099 bonds, 2 pseudobonds, 1845 residues, 5 models selected
> select add #2
13804 atoms, 14099 bonds, 2 pseudobonds, 1845 residues, 5 models selected
> select add #2
13804 atoms, 14099 bonds, 2 pseudobonds, 1845 residues, 5 models selected
> select add #2
13804 atoms, 14099 bonds, 2 pseudobonds, 1845 residues, 5 models selected
> volume #2 level 0.006595
> volume #2 level 0.01971
> volume #2 level 0.02194
> volume #2 style image
> fitmap #1 inMap #2
Fit molecule PKS13-dimer-fit172-coot.pdb (#1) to map
postprocess_masked_job165.mrc (#2) using 13804 atoms
average map value = 7.726e-05, steps = 340
shifted from previous position = 3.07
rotated from previous position = 8.58 degrees
atoms outside contour = 13803, contour level = 0.021939
Position of PKS13-dimer-fit172-coot.pdb (#1) relative to
postprocess_masked_job165.mrc (#2) coordinates:
Matrix rotation and translation
0.98990568 0.12309145 0.07025126 -13.80334558
-0.12251065 0.99238805 -0.01253358 -15.89148058
-0.07125928 0.00380053 0.99745059 81.80565718
Axis 0.05753000 0.49841120 -0.86502981
Axis point 188.01229388 90.41065786 0.00000000
Rotation angle (degrees) 8.16137364
Shift along axis -79.47893057
> fitmap #1 inMap #2
Fit molecule PKS13-dimer-fit172-coot.pdb (#1) to map
postprocess_masked_job165.mrc (#2) using 13804 atoms
average map value = 7.752e-05, steps = 100
shifted from previous position = 0.0984
rotated from previous position = 0.173 degrees
atoms outside contour = 13802, contour level = 0.021939
Position of PKS13-dimer-fit172-coot.pdb (#1) relative to
postprocess_masked_job165.mrc (#2) coordinates:
Matrix rotation and translation
0.98978408 0.12245790 0.07301736 -14.11747151
-0.12179306 0.99246362 -0.01350612 -15.85890939
-0.07412101 0.00447513 0.99723921 82.22734489
Axis 0.06293481 0.51498775 -0.85488410
Axis point 199.67137901 91.16105429 0.00000000
Rotation angle (degrees) 8.21315523
Shift along axis -79.35047435
> volume #2 style surface
> fitmap #1 inMap #2
Fit molecule PKS13-dimer-fit172-coot.pdb (#1) to map
postprocess_masked_job165.mrc (#2) using 13804 atoms
average map value = 7.773e-05, steps = 80
shifted from previous position = 0.0365
rotated from previous position = 0.068 degrees
atoms outside contour = 13802, contour level = 0.021939
Position of PKS13-dimer-fit172-coot.pdb (#1) relative to
postprocess_masked_job165.mrc (#2) coordinates:
Matrix rotation and translation
0.98973206 0.12221783 0.07411648 -14.25498805
-0.12152069 0.99249212 -0.01386084 -15.84597603
-0.07525406 0.00471183 0.99715326 82.39364484
Axis 0.06483288 0.52141802 -0.85083485
Axis point 204.15094991 91.72640025 0.00000000
Rotation angle (degrees) 8.23508057
Shift along axis -79.28995391
> fitmap #1 inMap #2
Fit molecule PKS13-dimer-fit172-coot.pdb (#1) to map
postprocess_masked_job165.mrc (#2) using 13804 atoms
average map value = 7.754e-05, steps = 156
shifted from previous position = 0.0447
rotated from previous position = 0.0701 degrees
atoms outside contour = 13802, contour level = 0.021939
Position of PKS13-dimer-fit172-coot.pdb (#1) relative to
postprocess_masked_job165.mrc (#2) coordinates:
Matrix rotation and translation
0.98978322 0.12251542 0.07293255 -14.11605428
-0.12182819 0.99245506 -0.01381478 -15.79978712
-0.07407480 0.00478839 0.99724119 82.15549352
Axis 0.06509978 0.51443631 -0.85505398
Axis point 199.58510626 89.72853709 0.00000000
Rotation angle (degrees) 8.21464848
Shift along axis -79.29431760
> volume #2 level 0.0166
> select add #2
13804 atoms, 14099 bonds, 2 pseudobonds, 1845 residues, 5 models selected
> select add #2
13804 atoms, 14099 bonds, 2 pseudobonds, 1845 residues, 5 models selected
> select add #2
13804 atoms, 14099 bonds, 2 pseudobonds, 1845 residues, 5 models selected
> select add #3
14818 atoms, 15127 bonds, 2 pseudobonds, 1985 residues, 6 models selected
> select add #2
14818 atoms, 15127 bonds, 2 pseudobonds, 1985 residues, 6 models selected
> select add #2
14818 atoms, 15127 bonds, 2 pseudobonds, 1985 residues, 6 models selected
> select add #2
14818 atoms, 15127 bonds, 2 pseudobonds, 1985 residues, 6 models selected
> select #1/A
6900 atoms, 7047 bonds, 1 pseudobond, 922 residues, 2 models selected
> select add #1.1
6900 atoms, 7047 bonds, 2 pseudobonds, 922 residues, 2 models selected
> select add #1
13804 atoms, 14099 bonds, 2 pseudobonds, 1845 residues, 2 models selected
> view matrix models
> #1,0.98978,0.12252,0.072933,-15.068,-0.12183,0.99246,-0.013815,21.511,-0.074075,0.0047884,0.99724,12.428
> select add #3
14818 atoms, 15127 bonds, 2 pseudobonds, 1985 residues, 3 models selected
> select subtract #1.1
14818 atoms, 15127 bonds, 1985 residues, 2 models selected
> select add #1
14818 atoms, 15127 bonds, 2 pseudobonds, 1985 residues, 3 models selected
> view matrix models
> #1,0.98978,0.12252,0.072933,-23.918,-0.12183,0.99246,-0.013815,19.099,-0.074075,0.0047884,0.99724,-18.697,#3,0.17304,0.46347,-0.86905,220,0.93655,-0.35052,-0.00045762,143.16,-0.30484,-0.81384,-0.49472,146.55
> undo
> select subtract #1.1
14818 atoms, 15127 bonds, 1985 residues, 2 models selected
> select add #1
14818 atoms, 15127 bonds, 2 pseudobonds, 1985 residues, 3 models selected
> select subtract #1
1014 atoms, 1028 bonds, 140 residues, 1 model selected
> view matrix models
> #3,0.17304,0.46347,-0.86905,197.39,0.93655,-0.35052,-0.00045762,162.77,-0.30484,-0.81384,-0.49472,103.56
> view matrix models
> #3,0.17304,0.46347,-0.86905,197.72,0.93655,-0.35052,-0.00045762,167.16,-0.30484,-0.81384,-0.49472,100.86
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.51648,0.71683,-0.46841,197.81,0.5625,0.12842,0.81676,167.47,0.64563,-0.68532,-0.33689,100.8
> view matrix models
> #3,0.6418,0.51409,-0.56904,197.31,0.56657,0.18219,0.80362,167.66,0.5168,-0.83817,-0.17433,100.11
> view matrix models
> #3,0.75378,0.26074,-0.60318,196.55,0.65712,-0.30071,0.6912,166.31,-0.0011631,-0.91738,-0.39801,100.32
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.75378,0.26074,-0.60318,231.13,0.65712,-0.30071,0.6912,206.75,-0.0011631,-0.91738,-0.39801,124.25
> view matrix models
> #3,0.75378,0.26074,-0.60318,230.22,0.65712,-0.30071,0.6912,203.61,-0.0011631,-0.91738,-0.39801,124.8
> view matrix models
> #3,0.75378,0.26074,-0.60318,230.69,0.65712,-0.30071,0.6912,204.09,-0.0011631,-0.91738,-0.39801,125.16
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.28296,0.33086,-0.90026,231.46,0.89576,0.24436,0.37135,206.22,0.34286,-0.91149,-0.22722,124.84
> view matrix models
> #3,0.30168,0.28903,-0.90854,231.34,0.88909,0.25879,0.37755,206.26,0.34424,-0.92168,-0.1789,124.73
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.30168,0.28903,-0.90854,227.76,0.88909,0.25879,0.37755,205.21,0.34424,-0.92168,-0.1789,120.46
> fitmap #1 inMap #2
Fit molecule PKS13-dimer-fit172-coot.pdb (#1) to map
postprocess_masked_job165.mrc (#2) using 13804 atoms
average map value = 0.03415, steps = 192
shifted from previous position = 24.9
rotated from previous position = 8.64 degrees
atoms outside contour = 2387, contour level = 0.016602
Position of PKS13-dimer-fit172-coot.pdb (#1) relative to
postprocess_masked_job165.mrc (#2) coordinates:
Matrix rotation and translation
0.99997366 -0.00306661 -0.00657844 1.94389289
0.00314955 0.99991521 0.01263518 -3.10769032
0.00653914 -0.01265556 0.99989853 1.18641658
Axis -0.86729528 -0.44984128 0.21317064
Axis point 0.00000000 92.35013017 247.82308798
Rotation angle (degrees) 0.83541559
Shift along axis -0.03505255
> fitmap #3 inMap #2
Fit molecule
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
to map postprocess_masked_job165.mrc (#2) using 1014 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 1014, contour level = 0.016602
Position of
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
relative to postprocess_masked_job165.mrc (#2) coordinates:
Matrix rotation and translation
0.30168327 0.28902720 -0.90854305 227.76088513
0.88909181 0.25878817 0.37755057 205.20729295
0.34424258 -0.92167888 -0.17889965 120.46175134
Axis -0.68309136 -0.65867275 0.31549389
Axis point 0.00000000 99.23822801 92.23364628
Rotation angle (degrees) 108.01187500
Shift along axis -252.74099945
> fitmap #3 inMap #2
Fit molecule
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
to map postprocess_masked_job165.mrc (#2) using 1014 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 1014, contour level = 0.016602
Position of
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
relative to postprocess_masked_job165.mrc (#2) coordinates:
Matrix rotation and translation
0.30168327 0.28902720 -0.90854305 227.76088513
0.88909181 0.25878817 0.37755057 205.20729295
0.34424258 -0.92167888 -0.17889965 120.46175134
Axis -0.68309136 -0.65867275 0.31549389
Axis point 0.00000000 99.23822801 92.23364628
Rotation angle (degrees) 108.01187500
Shift along axis -252.74099945
> fitmap #3 inMap #2
Fit molecule
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
to map postprocess_masked_job165.mrc (#2) using 1014 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 1014, contour level = 0.016602
Position of
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
relative to postprocess_masked_job165.mrc (#2) coordinates:
Matrix rotation and translation
0.30168327 0.28902720 -0.90854305 227.76088513
0.88909181 0.25878817 0.37755057 205.20729295
0.34424258 -0.92167888 -0.17889965 120.46175134
Axis -0.68309136 -0.65867275 0.31549389
Axis point 0.00000000 99.23822801 92.23364628
Rotation angle (degrees) 108.01187500
Shift along axis -252.74099945
> fitmap #3 inMap #2
Fit molecule
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
to map postprocess_masked_job165.mrc (#2) using 1014 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 1014, contour level = 0.016602
Position of
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
relative to postprocess_masked_job165.mrc (#2) coordinates:
Matrix rotation and translation
0.30168327 0.28902720 -0.90854305 227.76088513
0.88909181 0.25878817 0.37755057 205.20729295
0.34424258 -0.92167888 -0.17889965 120.46175134
Axis -0.68309136 -0.65867275 0.31549389
Axis point 0.00000000 99.23822801 92.23364628
Rotation angle (degrees) 108.01187500
Shift along axis -252.74099945
> fitmap #3 inMap #2
Fit molecule
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
to map postprocess_masked_job165.mrc (#2) using 1014 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 1014, contour level = 0.016602
Position of
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
relative to postprocess_masked_job165.mrc (#2) coordinates:
Matrix rotation and translation
0.30168327 0.28902720 -0.90854305 227.76088513
0.88909181 0.25878817 0.37755057 205.20729295
0.34424258 -0.92167888 -0.17889965 120.46175134
Axis -0.68309136 -0.65867275 0.31549389
Axis point 0.00000000 99.23822801 92.23364628
Rotation angle (degrees) 108.01187500
Shift along axis -252.74099945
> view matrix models
> #3,0.30168,0.28903,-0.90854,190.11,0.88909,0.25879,0.37755,188.26,0.34424,-0.92168,-0.1789,132.89
> view matrix models
> #3,0.30168,0.28903,-0.90854,169.97,0.88909,0.25879,0.37755,203.27,0.34424,-0.92168,-0.1789,134.63
> view matrix models
> #3,0.30168,0.28903,-0.90854,161.86,0.88909,0.25879,0.37755,215.91,0.34424,-0.92168,-0.1789,140.84
> view matrix models
> #3,0.30168,0.28903,-0.90854,166.67,0.88909,0.25879,0.37755,229.54,0.34424,-0.92168,-0.1789,151.34
> view matrix models
> #3,0.30168,0.28903,-0.90854,167.18,0.88909,0.25879,0.37755,227.6,0.34424,-0.92168,-0.1789,156.39
> view matrix models
> #3,0.30168,0.28903,-0.90854,180.6,0.88909,0.25879,0.37755,222.14,0.34424,-0.92168,-0.1789,147.26
> fitmap #3 inMap #2
Fit molecule
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
to map postprocess_masked_job165.mrc (#2) using 1014 atoms
average map value = 0.008591, steps = 188
shifted from previous position = 5.37
rotated from previous position = 17.7 degrees
atoms outside contour = 865, contour level = 0.016602
Position of
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
relative to postprocess_masked_job165.mrc (#2) coordinates:
Matrix rotation and translation
0.48854900 0.46335453 -0.73933920 177.69962119
0.76888632 0.17194262 0.61583241 221.96470094
0.41247266 -0.86933211 -0.27226456 151.82204047
Axis -0.77996767 -0.60490000 0.16045692
Axis point 0.00000000 131.66749802 60.70567951
Rotation angle (degrees) 107.81150403
Shift along axis -248.50551055
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.40766,0.71912,-0.56274,178.24,0.16898,0.54622,0.82042,222.94,0.89736,-0.42955,0.10115,152.51
> fitmap #3 inMap #2
Fit molecule
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
to map postprocess_masked_job165.mrc (#2) using 1014 atoms
average map value = 0.009305, steps = 80
shifted from previous position = 3.05
rotated from previous position = 6.94 degrees
atoms outside contour = 825, contour level = 0.016602
Position of
test_cd2bf_unrelaxed_rank_001_alphafold2_multimer_v3_model_1_seed_000.pdb (#3)
relative to postprocess_masked_job165.mrc (#2) coordinates:
Matrix rotation and translation
0.40037617 0.78026272 -0.48050911 180.51645256
0.07022789 0.49670286 0.86507474 222.03487856
0.91365582 -0.38010046 0.14407179 154.33609290
Axis -0.62271943 -0.69723007 -0.35509259
Axis point -38.16750354 0.00000000 5.97685817
Rotation angle (degrees) 88.82103254
Shift along axis -322.02409813
> transparency sel 80
> select add #2
1014 atoms, 1028 bonds, 140 residues, 4 models selected
> transparency (#3 & sel) 80
> transparency (#3 & sel) 90
> select add #2
1014 atoms, 1028 bonds, 140 residues, 4 models selected
> select subtract #3
3 models selected
> select add #2
3 models selected
> select add #2
3 models selected
> select add #2
3 models selected
> select add #2
3 models selected
> transparency #2.1 80
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-20.6.1
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640
OpenGL vendor: Intel Inc.
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro14,1
Processor Name: Dual-Core Intel Core i5
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 512.0.0.0.0
OS Loader Version: 577~170
SMC Version (system): 2.43f11
Software:
System Software Overview:
System Version: macOS 13.4 (22F66)
Kernel Version: Darwin 22.5.0
Time since boot: 8 days, 3 hours, 31 minutes
Graphics/Displays:
Intel Iris Plus Graphics 640:
Chipset Model: Intel Iris Plus Graphics 640
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x5926
Revision ID: 0x0006
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
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
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 19 months ago
| Component: | Unassigned → Graphics |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Graphics hardware encountered an error and was reset |
comment:2 by , 19 months ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
| Summary: | Graphics hardware encountered an error and was reset → Graphics crash, macOS 13.4, Intel Iris Plus Graphics 640 |
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Apple Intel graphics driver crash.