#14805 closed defect (nonchimerax)

Graphics crash, macOS 13.4, Intel Iris Plus Graphics 640

Reported by: chimerax-bug-report@… 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 Eric Pettersen)

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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===== 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 Eric Pettersen, 19 months ago

Component: UnassignedGraphics
Description: modified (diff)
Owner: set to Tom Goddard
Platform: all
Project: ChimeraX
Status: newassigned
Summary: ChimeraX bug report submissionGraphics hardware encountered an error and was reset

comment:2 by Tom Goddard, 19 months ago

Resolution: nonchimerax
Status: assignedclosed
Summary: Graphics hardware encountered an error and was resetGraphics crash, macOS 13.4, Intel Iris Plus Graphics 640

Apple Intel graphics driver crash.

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