The following bug report has been submitted:
Platform: Windows-10-10.0.26100
ChimeraX Version: 1.10rc202505070250 (2025-05-07 02:50:46 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Current thread 0x00006b44 (most recent call first):
File "C:\Program Files\ChimeraX 1.10rc202505070250\bin\Lib\site-packages\chimerax\ui\widgets\htmlview.py", line 237 in setHtml
File "C:\Program Files\ChimeraX 1.10rc202505070250\bin\Lib\site-packages\chimerax\log\tool.py", line 462 in _actually_show
File "C:\Program Files\ChimeraX 1.10rc202505070250\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "C:\Program Files\ChimeraX 1.10rc202505070250\bin\Lib\site-packages\chimerax\core\__main__.py", line 1057 in init
File "C:\Program Files\ChimeraX 1.10rc202505070250\bin\Lib\site-packages\chimerax\core\__main__.py", line 1220 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: _win32sysloader, win32api, win32com.shell.shell, chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.pdb_lib._load_libs, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, PIL._imaging, PIL._imagingmath, psutil._psutil_windows, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.morph._morph (total: 61)
===== Log before crash start =====
> open "F:/structure/cxs/0904 analyse ISGlation site.cxs"
> view name session-start
opened ChimeraX session
> select add #2
35937 atoms, 36690 bonds, 15 pseudobonds, 4473 residues, 2 models selected
> select subtract #2
Nothing selected
> lighting flat
> lighting simple
> lighting soft
> lighting full
> lighting soft
> select #2/A:2309
8 atoms, 7 bonds, 1 residue, 1 model selected
> open D:/桌面/mRNF213.pdb
Chain information for mRNF213.pdb #5
---
Chain | Description
A | No description available
Computing secondary structure
> color #5 #55ff7fff
> color #5 #55aa7fff
> color #5 #55ff7fff
> ui tool show Matchmaker
> matchmaker #!5 to #2
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 J79.pdb, chain A (#2) with mRNF213.pdb, chain A (#5), sequence
alignment score = 15825.6
RMSD between 1155 pruned atom pairs is 1.263 angstroms; (across all 4359
pairs: 6.603)
> hide #!2 models
> select #5/A:483,720,1128,927,1296,2133,2309,2898,2906,2909
86 atoms, 76 bonds, 10 residues, 1 model selected
> color sel red
> style sel sphere
Changed 86 atom styles
> style sel sphere
Changed 86 atom styles
> show sel atoms
> select add #5
35235 atoms, 35955 bonds, 15 pseudobonds, 4420 residues, 3 models selected
> select subtract #5
Nothing selected
> save "D:/桌面/ISG site.cxs"
> close #5
> close #4
> close #3
> close #2
> close #1
> open 1tnd
Summary of feedback from opening 1tnd fetched from pdb
---
notes | Fetching compressed mmCIF 1tnd from http://files.rcsb.org/download/1tnd.cif
Fetching CCD CAC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/CAC/CAC.cif
Fetching CCD GSP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/GSP/GSP.cif
1tnd title:
The 2.2 angstroms crystal structure of transducin-α complexed with GTP γ S
[more info...]
Chain information for 1tnd #1
---
Chain | Description | UniProt
A B C | TRANSDUCIN | GNAT1_BOVIN 27-350
Non-standard residues in 1tnd #1
---
CAC — cacodylate ion (dimethylarsinate)
GSP — 5'-guanosine-diphosphate-monothiophosphate
MG — magnesium ion
1tnd mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
> open 1tag
Summary of feedback from opening 1tag fetched from pdb
---
notes | Fetching compressed mmCIF 1tag from http://files.rcsb.org/download/1tag.cif
Fetching CCD GDP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/GDP/GDP.cif
1tag title:
Structural determinants for activation of the α-subunit of A heterotrimeric G
protein [more info...]
Chain information for 1tag #2
---
Chain | Description | UniProt
A | TRANSDUCIN-ALPHA | GNAT1_BOVIN 27-350
Non-standard residues in 1tag #2
---
GDP — guanosine-5'-diphosphate
MG — magnesium ion
> delete solvent
> delete :.b-c
Missing or invalid "atoms" argument: invalid atoms specifier
> morph #1 #2
models have different number of chains, 3 (Morph - 1tnd #/A,Morph - 1tnd
#/B,Morph - 1tnd #/C) and 1 (1tag #2/A)
> select #1/B
2574 atoms, 2618 bonds, 7 pseudobonds, 320 residues, 2 models selected
> delete
Missing or invalid "atoms" argument: empty atom specifier
> hide #!1 models
> hide #!2 models
> open "F:/structure/all map/182/182.pdb"
Chain information for 182.pdb #3
---
Chain | Description
A | No description available
D | No description available
Computing secondary structure
> select add #3
15936 atoms, 16260 bonds, 19 pseudobonds, 1988 residues, 4 models selected
> select subtract #3
2574 atoms, 2618 bonds, 7 pseudobonds, 320 residues, 2 models selected
> open F:/structure/细节结构/79AAA.pdb
Chain information for 79AAA.pdb #4
---
Chain | Description
A | No description available
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #!4 to #3
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 182.pdb, chain A (#3) with 79AAA.pdb, chain A (#4), sequence
alignment score = 6785.5
RMSD between 302 pruned atom pairs is 1.046 angstroms; (across all 1504 pairs:
15.976)
> morph #3,4
models have different number of chains, 2 (Morph - 182.pdb #/A,Morph - 182.pdb
#/D) and 1 (79AAA.pdb #4/A)
> select #3/D
1205 atoms, 1225 bonds, 157 residues, 1 model selected
> open "F:/structure/细节结构/182AAA only.pdb"
Chain information for 182AAA only.pdb #5
---
Chain | Description
A | No description available
Computing secondary structure
> hide #!4 models
> show #!4 models
> hide #!3 models
> select add #3
13362 atoms, 13642 bonds, 12 pseudobonds, 1668 residues, 2 models selected
> select subtract #3
Nothing selected
> morph #4,5
Computed 51 frame morph #6
> coordset #6 1,51
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!3 models
> color #6 #ff5500ff
> hide #!3 models
> select ::name="ATP"
217 atoms, 231 bonds, 7 residues, 3 models selected
> show #!6 atoms
> hide #!6 atoms
> select ::name="ATP"
217 atoms, 231 bonds, 7 residues, 3 models selected
> select ::name="ATP"
217 atoms, 231 bonds, 7 residues, 3 models selected
> show #!6 atoms
> hide #!6 atoms
> select add #5
12281 atoms, 12549 bonds, 12 pseudobonds, 1515 residues, 4 models selected
> select subtract #5
124 atoms, 132 bonds, 4 residues, 2 models selected
> hide #!6 models
> select add #4
12956 atoms, 13251 bonds, 2 pseudobonds, 1608 residues, 3 models selected
> select subtract #4
93 atoms, 99 bonds, 3 residues, 1 model selected
> select add #3
13362 atoms, 13642 bonds, 12 pseudobonds, 1668 residues, 2 models selected
> select subtract #3
Nothing selected
> show #!3 models
> show #!4 models
> show #!5 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> show #!6 models
> open "F:/ISG 182.pdb"
Chain information for ISG 182.pdb #7
---
Chain | Description
D | No description available
Computing secondary structure
> color #7 #aaff7fff
> color #7 #aaff00ff
> open F:/structure/细节结构/79AAA1.pdb
Chain information for 79AAA1.pdb #8
---
Chain | Description
A | No description available
Computing secondary structure
> hide #!6 models
> ui tool show Matchmaker
> matchmaker #!3,5 to #8
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 79AAA1.pdb, chain A (#8) with 182.pdb, chain A (#3), sequence
alignment score = 750.6
RMSD between 140 pruned atom pairs is 0.735 angstroms; (across all 156 pairs:
11.086)
Matchmaker 79AAA1.pdb, chain A (#8) with 182AAA only.pdb, chain A (#5),
sequence alignment score = 750.6
RMSD between 140 pruned atom pairs is 0.735 angstroms; (across all 156 pairs:
11.086)
> show #!3 models
> show #!5 models
> ui tool show Matchmaker
> matchmaker #!4 to #8
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 79AAA1.pdb, chain A (#8) with 79AAA.pdb, chain A (#4), sequence
alignment score = 812.4
RMSD between 140 pruned atom pairs is 0.000 angstroms; (across all 156 pairs:
10.962)
> ui tool show Matchmaker
> matchmaker #7 to #3
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 182.pdb, chain D (#3) with ISG 182.pdb, chain D (#7), sequence
alignment score = 771.9
RMSD between 157 pruned atom pairs is 0.000 angstroms; (across all 157 pairs:
0.000)
> hide #!8 models
> show #!4 models
> hide #!3 models
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> morph #4,5
Computed 51 frame morph #9
> coordset #9 1,51
> color #9 #ffaa00ff
> color #9 #ff5500ff
> color #9 #ff557fff
> color #9 red
> color #9 #ff814fff
> hide #7 models
> show #7 models
> hide #!9 models
> show #!6 models
> ui tool show Matchmaker
> matchmaker #!4 to #6
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 Morph - 79AAA.pdb, chain A (#6) with 79AAA.pdb, chain A (#4),
sequence alignment score = 7477.9
RMSD between 397 pruned atom pairs is 1.069 angstroms; (across all 1504 pairs:
11.312)
> ui tool show Matchmaker
> matchmaker #!3 to #6
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 Morph - 79AAA.pdb, chain A (#6) with 182.pdb, chain A (#3),
sequence alignment score = 6795.1
RMSD between 306 pruned atom pairs is 1.043 angstroms; (across all 1504 pairs:
15.656)
> ui tool show Matchmaker
> matchmaker #7 to #3
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 182.pdb, chain D (#3) with ISG 182.pdb, chain D (#7), sequence
alignment score = 771.9
RMSD between 157 pruned atom pairs is 0.000 angstroms; (across all 157 pairs:
0.000)
> save F:/structure/细节结构/Morph.cxs
> open "F:/79 ISG.pdb"
Chain information for 79 ISG.pdb #10
---
Chain | Description
A | No description available
D | No description available
Computing secondary structure
> select add #10
14067 atoms, 14377 bonds, 2 pseudobonds, 1761 residues, 2 models selected
> select subtract #10
Nothing selected
> select #10/D
1205 atoms, 1225 bonds, 157 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #10,1,0,0,6.9278,0,1,0,58.652,0,0,1,14.873
> view matrix models #10,1,0,0,8.0617,0,1,0,88.98,0,0,1,30.342
> view matrix models #10,1,0,0,8.282,0,1,0,86.663,0,0,1,28.185
> color #10 white
> color #10 #aaffffff
> ui tool show Matchmaker
> matchmaker #!3 to #10
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 79 ISG.pdb, chain A (#10) with 182.pdb, chain A (#3), sequence
alignment score = 6785.5
RMSD between 302 pruned atom pairs is 1.046 angstroms; (across all 1504 pairs:
15.976)
> show #!3 models
> morph #3,10
Computed 51 frame morph #11
> coordset #11 1,51
> morph #10,3
Computed 51 frame morph #12
> coordset #12 1,51
> hide #!6 models
> hide #7 models
> hide #!11 models
> hide #!12 models
> close #10
> close #11
> close #12
> open "F:/79 ISG.pdb"
Chain information for 79 ISG.pdb #10
---
Chain | Description
A | No description available
D | No description available
Computing secondary structure
> color #10 #aaff00ff
> color #10 #aaff7fff
> show #!3 models
> ui tool show Matchmaker
> matchmaker #!3 to #10
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 79 ISG.pdb, chain A (#10) with 182.pdb, chain A (#3), sequence
alignment score = 6785.5
RMSD between 302 pruned atom pairs is 1.046 angstroms; (across all 1504 pairs:
15.976)
> morph #10,3
Computed 51 frame morph #11
> coordset #11 1,51
> select #11/A
12053 atoms, 12310 bonds, 12 pseudobonds, 1504 residues, 2 models selected
> color (#!11 & sel) orange
> color (#!11 & sel) #ff0000ff
> color (#!11 & sel) #ff45b5ff
> color (#!11 & sel) #ff45aeff
> color (#!11 & sel) #ff108bff
> color (#!11 & sel) #ff3613ff
> color (#!11 & sel) #ff7d31ff
> color (#!11 & sel) #ff9752ff
> color (#!11 & sel) #ff8961ff
> color (#!11 & sel) #ff8962ff
> select add #11
13258 atoms, 13535 bonds, 12 pseudobonds, 1661 residues, 2 models selected
> select subtract #11
Nothing selected
> select ::name="ATP"
341 atoms, 363 bonds, 11 residues, 5 models selected
> show #!11 atoms
> hide #!11 atoms
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #!11 models
> show #!11 models
> select #7/D
1205 atoms, 1225 bonds, 157 residues, 1 model selected
> hide sel cartoons
> select #11/A:1813-1967
1212 atoms, 1244 bonds, 155 residues, 1 model selected
> color sel #f9fbfcff
> color sel #f9f9f9ff
> color sel #f4f4f4ff
> color sel #f8f8f8ff
> color sel #ffffffff
> color sel #ff6c5bff
> color sel #5b5b5bff
> color sel #f0f0f0ff
> color sel #ffffffff
> color sel #f6f9fbff
> color sel #f7f7f7ff
> color sel #f0f0f0ff
> color sel #ffffffff
> color sel #280000ff
> color sel #d3d3d3ff
> color sel #ffffffff
> color sel #f9f9f9ff
> color sel #d61008ff
> color sel #a0483bff
> color sel #fdfdfdff
> color sel #dec4c1ff
> color sel #ff6c5bff
> select #11/A:1967-2268
2141 atoms, 2191 bonds, 3 pseudobonds, 260 residues, 2 models selected
> color (#!11 & sel) #ffffffff
> color (#!11 & sel) #eff4f8ff
> color (#!11 & sel) #f1f1f1ff
> color (#!11 & sel) #f0f0f0ff
> color (#!11 & sel) #f4f4f4ff
> color (#!11 & sel) #f5f5f5ff
> color (#!11 & sel) #f4f4f4ff
> color (#!11 & sel) #ffffffff
> color (#!11 & sel) #ffd5d1ff
> color (#!11 & sel) #ff6d5cff
> color (#!11 & sel) #d61008ff
> select #11/A:2268-2395
827 atoms, 847 bonds, 1 pseudobond, 102 residues, 2 models selected
> color (#!11 & sel) #ffffffff
> color (#!11 & sel) #f1f6cfff
> color (#!11 & sel) #f3f3f3ff
> color (#!11 & sel) #ffffffff
> color (#!11 & sel) #f0f0f0ff
> color (#!11 & sel) #e5e8e5ff
> color (#!11 & sel) #eeeeeeff
> color (#!11 & sel) #ffffffff
> color (#!11 & sel) #d4d0d0ff
> select #11/A:2395-2744
2605 atoms, 2649 bonds, 2 pseudobonds, 328 residues, 2 models selected
> color (#!11 & sel) #ffffffff
> color (#!11 & sel) #297cd1ff
> color (#!11 & sel) #787878ff
> color (#!11 & sel) #f7f7f7ff
> color (#!11 & sel) #ff533aff
> color (#!11 & sel) #f5f5f5ff
> color (#!11 & sel) #ffffffff
> color (#!11 & sel) #ff533aff
> color (#!11 & sel) #9c3e1fff
> select #11/A:2744-3001
1926 atoms, 1964 bonds, 1 pseudobond, 251 residues, 2 models selected
> color (#!11 & sel) #f0f0f0ff
> color (#!11 & sel) #a2cbf5ff
> color (#!11 & sel) #b9b9b9ff
> color (#!11 & sel) #edededff
> color (#!11 & sel) #f8f8f8ff
> color (#!11 & sel) #ffffffff
> color (#!11 & sel) #ffa295ff
> color (#!11 & sel) #ff533aff
> color (#!11 & sel) #ffffffff
> color (#!11 & sel) #c8adc1ff
> color (#!11 & sel) #f6f6f6ff
> color (#!11 & sel) #ffffffff
> color (#!11 & sel) #fcfcfcff
> color (#!11 & sel) #ffffffff
> color (#!11 & sel) #ff7b74ff
> color (#!11 & sel) #ff533aff
> color (#!11 & sel) #ff7b74ff
> select #11/A:3291-3447
1275 atoms, 1302 bonds, 156 residues, 1 model selected
> color sel #ffffffff
> color sel #ca7b29ff
> color sel #7878a2ff
> color sel #f0f0f0ff
> color sel #eeeeeeff
> color sel #ffffffff
> color sel #f9f9f9ff
> color sel #ffffffff
> color sel #e8716aff
> color sel #ff7b74ff
> color sel #d96847ff
> color sel #d86341ff
> select add #11
13258 atoms, 13535 bonds, 12 pseudobonds, 1661 residues, 2 models selected
> select subtract #11
Nothing selected
> movie record
> turn y 360 60
> morph play
Missing or invalid "structures" argument: invalid structures specifier
> movie stop
> movie encode induction_fit_with_rotation.mp4
Movie saved to induction_fit_with_rotation.mp4
> save "F:/structure/cxs/0906 morph.cxs"
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\张叶/Desktop\movie1.mp4
Movie saved to C:\Users\张叶/Desktop\movie1.mp4
> hide #7 models
> hide #!11 models
> show #!3 models
> hide #!3 models
> show #!11 models
> show #7 models
> hide #!11 models
> show #!10 models
> select #10/D
1205 atoms, 1225 bonds, 157 residues, 1 model selected
> view matrix models #10,1,0,0,-0.056219,0,1,0,-2.0534,0,0,1,1.6673
> undo
> ui mousemode right "move picked models"
> view matrix models #10,1,0,0,-0.084299,0,1,0,-0.68204,0,0,1,-0.01894
> undo
> ui mousemode right "translate selected models"
> view matrix models #10,1,0,0,0.00044511,0,1,0,0.48522,0,0,1,-0.50606
> undo
> ui mousemode right select
> ui mousemode right rotate
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> ui mousemode right "move picked models"
> ui mousemode right "translate selected atoms"
> select add #10
14067 atoms, 14377 bonds, 2 pseudobonds, 1761 residues, 2 models selected
> select subtract #10
Nothing selected
> select #10/A
12862 atoms, 13152 bonds, 2 pseudobonds, 1604 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> hide #7 models
> show #7 models
> hide #!10 models
> show #!10 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #!3 models
> morph #3,10
Computed 51 frame morph #12
> coordset #12 1,51
> morph #10,3
Computed 51 frame morph #13
> coordset #13 1,51
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> morph #10,3
Computed 51 frame morph #14
> coordset #14 1,51
> select add #10
14067 atoms, 14377 bonds, 2 pseudobonds, 1761 residues, 2 models selected
> select subtract #10
Nothing selected
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!12 models
> hide #!13 models
> hide #!14 models
> select #10/A
12862 atoms, 13152 bonds, 2 pseudobonds, 1604 residues, 2 models selected
> show sel cartoons
> show #!3 models
> morph #10,3
Computed 51 frame morph #15
> coordset #15 1,51
> show #!10 models
> hide #!10 models
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #!15 models
> hide #7 models
> show #!9 models
> hide #!9 models
> show #!11 models
> show #10.1 target m
> hide #10.1 target m
> select subtract #10.1
12862 atoms, 13152 bonds, 1604 residues, 1 model selected
> select add #10
14067 atoms, 14377 bonds, 2 pseudobonds, 1761 residues, 2 models selected
> select subtract #10
Nothing selected
> hide #!10 models
> show #!11 target m
> view #11 clip false
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #9.1 models
> hide #!11 models
> show #!4 models
> show #!10 models
> ui tool show Matchmaker
> matchmaker #!10 to #4
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 79AAA.pdb, chain A (#4) with 79 ISG.pdb, chain A (#10), sequence
alignment score = 8279.5
RMSD between 1603 pruned atom pairs is 0.000 angstroms; (across all 1603
pairs: 0.000)
> morph #10,4
models have different number of chains, 2 (Morph - 79 ISG.pdb #/A,Morph - 79
ISG.pdb #/D) and 1 (79AAA.pdb #4/A)
> open "F:/structure/细节结构/79AAA ISG15.pdb"
Chain information for 79AAA ISG15.pdb #16
---
Chain | Description
A | No description available
D | No description available
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #!16 to #10
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 79 ISG.pdb, chain A (#10) with 79AAA ISG15.pdb, chain A (#16),
sequence alignment score = 8279.5
RMSD between 1603 pruned atom pairs is 0.000 angstroms; (across all 1603
pairs: 0.000)
> morph #16,10
Computed 51 frame morph #17
> coordset #17 1,51
> morph #10,16
Computed 51 frame morph #18
> coordset #18 1,51
> select #17/D
1205 atoms, 1225 bonds, 157 residues, 1 model selected
> hide sel cartoons
> hide #!17 models
> select add #17
14036 atoms, 14344 bonds, 2 pseudobonds, 1760 residues, 2 models selected
> select subtract #17
Nothing selected
> hide #!18 models
> close #17
> show #!18 models
> show #!3 models
> hide #!3 models
> show #!3 models
> ui tool show Matchmaker
> matchmaker #!3 to #18
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Morph - 79 ISG.pdb, chain A (#18) with 182.pdb, chain A (#3),
sequence alignment score = 6785.5
RMSD between 302 pruned atom pairs is 1.046 angstroms; (across all 1504 pairs:
15.976)
> hide #!4 models
> morph #3,18
Computed 51 frame morph #17
> coordset #17 1,51
> show #!18 models
> hide #!17 models
> close #17
> hide #!18 models
> show #!3 models
> show #!16 models
> color #16 #aaffffff
> morph #16,3
Computed 51 frame morph #17
> coordset #17 1,51
> select ::name="ATP"
372 atoms, 396 bonds, 12 residues, 6 models selected
> show #!17 atoms
> hide #!17 atoms
> show #7 models
> hide #7 models
> show #7 models
> select add #7
1577 atoms, 1621 bonds, 169 residues, 6 models selected
> select subtract #7
279 atoms, 297 bonds, 9 residues, 5 models selected
> select add #5
12343 atoms, 12615 bonds, 12 pseudobonds, 1517 residues, 6 models selected
> select subtract #5
186 atoms, 198 bonds, 6 residues, 4 models selected
> select add #4
13018 atoms, 13317 bonds, 2 pseudobonds, 1610 residues, 5 models selected
> select subtract #4
155 atoms, 165 bonds, 5 residues, 3 models selected
> select add #3
13424 atoms, 13708 bonds, 12 pseudobonds, 1670 residues, 4 models selected
> select subtract #3
62 atoms, 66 bonds, 2 residues, 2 models selected
> select add #10
14098 atoms, 14410 bonds, 2 pseudobonds, 1762 residues, 3 models selected
> select subtract #10
31 atoms, 33 bonds, 1 residue, 1 model selected
> select add #16
14068 atoms, 14377 bonds, 2 pseudobonds, 1762 residues, 2 models selected
> select subtract #16
Nothing selected
> show #!18 models
> hide #!17 models
> show #!17 models
> hide #!18 models
> select #17/D
1205 atoms, 1225 bonds, 157 residues, 1 model selected
> color sel #aaff7fff
> select #17/A:1813-1967
1212 atoms, 1244 bonds, 155 residues, 1 model selected
> color sel #ff6c5bff
> select #18/A:1813-1967
1212 atoms, 1244 bonds, 155 residues, 1 model selected
> select #18/A:1967-2268
2357 atoms, 2416 bonds, 1 pseudobond, 287 residues, 2 models selected
> color #7,17 #d61008ff
> select #18/A:1813-1967
1212 atoms, 1244 bonds, 155 residues, 1 model selected
> color #7,17 #ff6c5bff
> select #18/A:1813-1967
1212 atoms, 1244 bonds, 155 residues, 1 model selected
> select #17/A:1813-1967
1212 atoms, 1244 bonds, 155 residues, 1 model selected
> select #17/A:1967-2268
2141 atoms, 2191 bonds, 3 pseudobonds, 260 residues, 2 models selected
> color (#!17 & sel) #d61008ff
> select #17/A:2268-2395
827 atoms, 847 bonds, 1 pseudobond, 102 residues, 2 models selected
> color (#!17 & sel) dark gray
> select #17/A:2395-2744
2605 atoms, 2649 bonds, 2 pseudobonds, 328 residues, 2 models selected
> color (#!17 & sel) #ffffffff
> color (#!17 & sel) #eff4f8ff
> color (#!17 & sel) #fbfbfbff
> color (#!17 & sel) #f0f0f0ff
> color (#!17 & sel) #aaffffff
> color (#!17 & sel) #f0f0f0ff
> color (#!17 & sel) #f3f3f3ff
> color (#!17 & sel) #f2f2f2ff
> color (#!17 & sel) #9c3e1fff
> color (#!17 & sel) #b6715bff
> color (#!17 & sel) #9c3e1fff
> select #17/A:2744-3001
1926 atoms, 1964 bonds, 1 pseudobond, 251 residues, 2 models selected
> color (#!17 & sel) #ff533aff
> select #17/A:3001-3291
2110 atoms, 2152 bonds, 4 pseudobonds, 257 residues, 2 models selected
> color (#!17 & sel) #ff7b74ff
> select #17/A:3291-3447
1275 atoms, 1302 bonds, 156 residues, 1 model selected
> color sel #d86341ff
> select #17/D
1205 atoms, 1225 bonds, 157 residues, 1 model selected
> color sel #aaff7fff
> select add #17
13258 atoms, 13535 bonds, 12 pseudobonds, 1661 residues, 2 models selected
> select subtract #17
Nothing selected
> color #7 #aaaaffff
> hide #!17 models
> show #!18 models
> select #18/A:3291-3447
1275 atoms, 1302 bonds, 156 residues, 1 model selected
> color sel #d86341ff
> select #18/A:3001-3291
2364 atoms, 2418 bonds, 291 residues, 1 model selected
> color sel #ff7b74ff
> select #18/A:2744-3001
1980 atoms, 2020 bonds, 258 residues, 1 model selected
> color sel #ff533aff
> select #18/A:2395-2744
2773 atoms, 2821 bonds, 350 residues, 1 model selected
> color sel #9c3e1fff
> select #18/A:2268-2395
923 atoms, 947 bonds, 1 pseudobond, 112 residues, 2 models selected
> color (#!18 & sel) dark gray
> select #18/A:1967-2268
2357 atoms, 2416 bonds, 1 pseudobond, 287 residues, 2 models selected
> color (#!18 & sel) #d61008ff
> select #18/A:1813-1967
1212 atoms, 1244 bonds, 155 residues, 1 model selected
> color sel #ff6c5bff
> select add #18
14036 atoms, 14344 bonds, 2 pseudobonds, 1760 residues, 2 models selected
> select subtract #18
Nothing selected
> show #!17 models
> hide #!17 models
> hide #!18 models
> show #!17 models
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\张叶/Desktop\movie2.mp4
Movie saved to C:\Users\张叶/Desktop\movie2.mp4
> combine #17,18
Remapping chain ID 'A' in Morph - 79 ISG.pdb #18 to 'B'
Remapping chain ID 'D' in Morph - 79 ISG.pdb #18 to 'E'
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> close #19
> ui tool show "Selection Inspector"
> graphics silhouettes false
> hide #18.1 models
> hide #17.1 models
> hide #!17 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> hide #7 models
> show #!3 models
> hide #!3 models
> show #!18 models
> show #7 models
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\张叶/Desktop\movie3.mp4
Movie saved to C:\Users\张叶/Desktop\movie3.mp4
> hide #!18 models
> show #!18 models
> show #!17 models
> hide #!18 models
> coordinate sets morph
Unknown command: coordinate sets morph
> hide #!17 models
> show #!18 models
> hide #!18 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!16 models
> show #!3 models
> morph #16,3
Computed 51 frame morph #19
> coordset #19 1,51
> select #16/D
1205 atoms, 1225 bonds, 157 residues, 1 model selected
> color #7,19 #aaff7fff
> select #19/D
1205 atoms, 1225 bonds, 157 residues, 1 model selected
> color sel #aaff00ff
> color sel #aaff7fff
> select #19/A:1813-1967
1212 atoms, 1244 bonds, 155 residues, 1 model selected
> color sel #ff6c5bff
> select #19/A:1967-2268
2141 atoms, 2191 bonds, 3 pseudobonds, 260 residues, 2 models selected
> color (#!19 & sel) #d61008ff
> select #19/A:2268-2395
827 atoms, 847 bonds, 1 pseudobond, 102 residues, 2 models selected
> color (#!19 & sel) dark gray
> select #19/A:2395-2744
2605 atoms, 2649 bonds, 2 pseudobonds, 328 residues, 2 models selected
> color (#!19 & sel) #9c3e1fff
> select #19/A:2744-3001
1926 atoms, 1964 bonds, 1 pseudobond, 251 residues, 2 models selected
> color (#!19 & sel) #ff533aff
> select #19/A:3001-3291
2110 atoms, 2152 bonds, 4 pseudobonds, 257 residues, 2 models selected
> color (#!19 & sel) #ff7b74ff
> select #19/A:3291-3447
1275 atoms, 1302 bonds, 156 residues, 1 model selected
> color sel #d86341ff
> color #7 #ffaaffff
> color #7 #aaaaffff
> select add #19
13258 atoms, 13535 bonds, 12 pseudobonds, 1661 residues, 2 models selected
> select subtract #19
Nothing selected
> show #!18 models
> hide #!18 models
> hide #!19 models
> show #!19 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!19 models
> hide #!18 models
> show #!19 models
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\张叶/Desktop\movie4.mp4
Movie saved to C:\Users\张叶/Desktop\movie4.mp4
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!18 models
> hide #!18 models
> show #!19 models
> hide #!19 models
> hide #7 models
> show #!4 models
> select #3/A:3291-3447
1275 atoms, 1302 bonds, 156 residues, 1 model selected
> select #3/A:3291-3447
1275 atoms, 1302 bonds, 156 residues, 1 model selected
> color #4 red
> select #3/A:3291-3447
1275 atoms, 1302 bonds, 156 residues, 1 model selected
> select #3/A:1813-1967
1212 atoms, 1244 bonds, 155 residues, 1 model selected
> select #4/A:1813-1967
1212 atoms, 1244 bonds, 155 residues, 1 model selected
> color sel #ff6c5bff
> select #4/A:1967-2268
2357 atoms, 2416 bonds, 1 pseudobond, 287 residues, 2 models selected
> color (#!4 & sel) #d61008ff
> select #4/A:2268-2395
923 atoms, 947 bonds, 1 pseudobond, 112 residues, 2 models selected
> color (#!4 & sel) dark gray
> select #4/A:2395-2744
2773 atoms, 2821 bonds, 350 residues, 1 model selected
> color sel #9c3e1fff
> select #4/A:2744-3001
1980 atoms, 2020 bonds, 258 residues, 1 model selected
> color sel #ff533aff
> select #4/A:3001-3291
2364 atoms, 2418 bonds, 291 residues, 1 model selected
> color sel #ff7b74ff
> select #4/A:3291-3447
1275 atoms, 1302 bonds, 156 residues, 1 model selected
> color sel #d86341ff
> select add #4
12863 atoms, 13152 bonds, 2 pseudobonds, 1605 residues, 2 models selected
> select subtract #4
Nothing selected
> close #9
> close #6
> show #7 models
> hide #7 models
> show #!17 models
> hide #!17 models
> show #!17 models
> ui tool show Matchmaker
> matchmaker #!4 to #17
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 Morph - 79AAA ISG15.pdb, chain A (#17) with 79AAA.pdb, chain A
(#4), sequence alignment score = 7408.9
RMSD between 318 pruned atom pairs is 1.055 angstroms; (across all 1504 pairs:
15.044)
> hide #!17 models
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\张叶/Desktop\movie5.mp4
Movie saved to C:\Users\张叶/Desktop\movie5.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\张叶/Desktop\movie6.mp4
Movie saved to C:\Users\张叶/Desktop\movie6.mp4
> select ::name="ATP"
372 atoms, 396 bonds, 12 residues, 6 models selected
> color (#!4 & sel) #aaaaffff
> select #4/A:1
Nothing selected
> show #!17 models
> hide #!17 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #7 models
> show #!18 models
> hide #!4 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> hide #7 models
> show #!4 models
> show #7 models
> show #!18 models
> hide #!18 models
> hide #!4 models
> show #!19 models
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\张叶/Desktop\movie7.mp4
Movie saved to C:\Users\张叶/Desktop\movie7.mp4
> hide #!19 models
> hide #7 models
> show #!4 models
> show #7 models
> show #!17 models
> hide #!17 models
> show #!18 models
> hide #!4 models
> hide #!18 models
> show #!19 models
> hide #!19 models
> hide #7 models
> show #!4 models
> show #7 models
> show #!18 models
> hide #!4 models
> hide #!18 models
> show #!19 models
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\张叶/Desktop\movie8.mp4
Movie saved to C:\Users\张叶/Desktop\movie8.mp4
> hide #!19 models
> hide #7 models
> show #!4 models
> show #7 models
> show #!18 models
> hide #!4 models
> show #!19 models
> hide #!18 models
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\张叶/Desktop\movie9.mp4
Movie saved to C:\Users\张叶/Desktop\movie9.mp4
> save F:/structure/细节结构/vedio.cxs
> hide #!19 models
> show #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!16 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> select #16/D
1205 atoms, 1225 bonds, 157 residues, 1 model selected
> ui mousemode right "move picked models"
> view matrix models
> #16,0.9919,0.036478,0.12171,-88.805,0.056354,-0.98483,-0.1641,502.92,0.11388,0.16963,-0.97891,344.56
> ui mousemode right "translate selected atoms"
> ui tool show Matchmaker
> matchmaker #!3,16 to #8
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 79AAA1.pdb, chain A (#8) with 182.pdb, chain A (#3), sequence
alignment score = 750.6
RMSD between 140 pruned atom pairs is 0.735 angstroms; (across all 156 pairs:
11.086)
Matchmaker 79AAA1.pdb, chain A (#8) with 79AAA ISG15.pdb, chain A (#16),
sequence alignment score = 812.4
RMSD between 140 pruned atom pairs is 0.000 angstroms; (across all 156 pairs:
10.962)
> undo
> show #!3 models
> hide #!3 models
> show #!3 models
> ui tool show Matchmaker
> matchmaker #!3 to #4
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 79AAA.pdb, chain A (#4) with 182.pdb, chain A (#3), sequence
alignment score = 6785.5
RMSD between 302 pruned atom pairs is 1.046 angstroms; (across all 1504 pairs:
15.976)
> ui tool show Matchmaker
> matchmaker #!8 to #4
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 79AAA.pdb, chain A (#4) with 79AAA1.pdb, chain A (#8), sequence
alignment score = 812.4
RMSD between 140 pruned atom pairs is 0.000 angstroms; (across all 156 pairs:
10.962)
> ui tool show Matchmaker
> matchmaker #!8 to #3
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 182.pdb, chain A (#3) with 79AAA1.pdb, chain A (#8), sequence
alignment score = 750.6
RMSD between 140 pruned atom pairs is 0.735 angstroms; (across all 156 pairs:
11.086)
> show #!8 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> ui tool show Matchmaker
> matchmaker #!4 to #8
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 79AAA1.pdb, chain A (#8) with 79AAA.pdb, chain A (#4), sequence
alignment score = 812.4
RMSD between 140 pruned atom pairs is 0.000 angstroms; (across all 156 pairs:
10.962)
> show #!16 models
> ui tool show Matchmaker
> matchmaker #!8 to #16
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 79AAA ISG15.pdb, chain A (#16) with 79AAA1.pdb, chain A (#8),
sequence alignment score = 812.4
RMSD between 140 pruned atom pairs is 0.000 angstroms; (across all 156 pairs:
10.962)
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> ui tool show Matchmaker
> matchmaker #!3-4 to #8
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 79AAA1.pdb, chain A (#8) with 182.pdb, chain A (#3), sequence
alignment score = 750.6
RMSD between 140 pruned atom pairs is 0.735 angstroms; (across all 156 pairs:
11.086)
Matchmaker 79AAA1.pdb, chain A (#8) with 79AAA.pdb, chain A (#4), sequence
alignment score = 812.4
RMSD between 140 pruned atom pairs is 0.000 angstroms; (across all 156 pairs:
10.962)
> select #16/D
1205 atoms, 1225 bonds, 157 residues, 1 model selected
> ui mousemode right "move picked models"
> ui mousemode right "translate selected atoms"
> ui mousemode right "rotate selected models"
> view matrix models
> #16,0.98827,0.025396,0.1506,-86.003,0.048802,-0.98689,-0.15383,516.05,0.14472,0.15937,-0.97655,340.69
> open "F:/structure/细节结构/79AAA ISG15.pdb"
Chain information for 79AAA ISG15.pdb #6
---
Chain | Description
A | No description available
D | No description available
Computing secondary structure
> hide #!16 models
> ui tool show Matchmaker
> matchmaker #!6 to #8
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 79AAA1.pdb, chain A (#8) with 79AAA ISG15.pdb, chain A (#6),
sequence alignment score = 812.4
RMSD between 140 pruned atom pairs is 0.000 angstroms; (across all 156 pairs:
10.962)
> select #6/D
1205 atoms, 1225 bonds, 157 residues, 1 model selected
> ui mousemode right "translate selected atoms"
> select add #6
14068 atoms, 14377 bonds, 2 pseudobonds, 1762 residues, 2 models selected
> select subtract #6
Nothing selected
> Morph #6,3
Unknown command: Morph #6,3
> morph #6,3
Computed 51 frame morph #9
> coordset #9 1,51
> hide #!4 models
> hide #7 models
> hide #!9 models
> show #!9 models
> select #9/A:1813-1967
1212 atoms, 1244 bonds, 155 residues, 1 model selected
> color sel #ff6c5bff
> select #9/A:1967-2268
2141 atoms, 2191 bonds, 3 pseudobonds, 260 residues, 2 models selected
> color (#!9 & sel) #d61008ff
> select #9/A:2268-2395
827 atoms, 847 bonds, 1 pseudobond, 102 residues, 2 models selected
> color (#!9 & sel) dark gray
> select #9/A:2395-2744
2605 atoms, 2649 bonds, 2 pseudobonds, 328 residues, 2 models selected
> color (#!9 & sel) #9c3e1fff
> select #9/A:2744-3001
1926 atoms, 1964 bonds, 1 pseudobond, 251 residues, 2 models selected
> color (#!9 & sel) #ff533aff
> select #9/A:3001-3291
2110 atoms, 2152 bonds, 4 pseudobonds, 257 residues, 2 models selected
> color (#!9 & sel) #ff7b74ff
> select #9/A:3291-3447
1275 atoms, 1302 bonds, 156 residues, 1 model selected
> color sel #d86341ff
> select #9/A:3
Nothing selected
> select #9/D
1205 atoms, 1225 bonds, 157 residues, 1 model selected
> color sel #aaff7fff
> show #7 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> select add #9
13258 atoms, 13535 bonds, 12 pseudobonds, 1661 residues, 2 models selected
> select subtract #9
Nothing selected
> show #!4 models
> show #!16 models
> hide #!16 models
> show #!6 models
> open "F:/structure/细节结构/79AAA ISG15.pdb"
Chain information for 79AAA ISG15.pdb #20
---
Chain | Description
A | No description available
D | No description available
Computing secondary structure
> hide #!20 models
> show #!20 models
> color #20 #ffff7fff
> ui tool show Matchmaker
> matchmaker #!20 to #8
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 79AAA1.pdb, chain A (#8) with 79AAA ISG15.pdb, chain A (#20),
sequence alignment score = 812.4
RMSD between 140 pruned atom pairs is 0.000 angstroms; (across all 156 pairs:
10.962)
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> morph #20,6
Computed 51 frame morph #21
> coordset #21 1,51
> close #21
> show #!20 models
> morph #6,20
Computed 51 frame morph #21
> coordset #21 1,51
> hide #7 models
> show #7 models
> hide #!21 models
> show #!20 models
> show #!3 models
> morph #20,3
Computed 51 frame morph #22
> coordset #22 1,51
> show #!4 models
> hide #!4 models
> show #!4 models
> select #22/A:1813-1967
1212 atoms, 1244 bonds, 155 residues, 1 model selected
> color sel #ff6c5bff
> select #22/A:1967-2268
2141 atoms, 2191 bonds, 3 pseudobonds, 260 residues, 2 models selected
> color (#!22 & sel) #d61008ff
> select #22/A:2268-2395
827 atoms, 847 bonds, 1 pseudobond, 102 residues, 2 models selected
> color (#!22 & sel) dark gray
> select #22/A:2395-2744
2605 atoms, 2649 bonds, 2 pseudobonds, 328 residues, 2 models selected
> color (#!22 & sel) #9c3e1fff
> select #22/A:2744-3001
1926 atoms, 1964 bonds, 1 pseudobond, 251 residues, 2 models selected
> color (#!22 & sel) #ff533aff
> select #22/A:3001-3291
2110 atoms, 2152 bonds, 4 pseudobonds, 257 residues, 2 models selected
> color (#!22 & sel) #ff7b74ff
> select #22/A:3291-3447
1275 atoms, 1302 bonds, 156 residues, 1 model selected
> color sel #d86341ff
> select #22/D
1205 atoms, 1225 bonds, 157 residues, 1 model selected
> color sel #aaff7fff
> hide #!22 models
> show #!21 models
> select #21/D
1205 atoms, 1225 bonds, 157 residues, 1 model selected
> color sel #aaff00ff
> color sel #aaff7fff
> select add #21
14068 atoms, 14377 bonds, 2 pseudobonds, 1762 residues, 2 models selected
> select subtract #21
Nothing selected
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> hide #7 models
> show #7 models
> show #!21 models
> hide #!21 models
> hide #7 models
> show #7 models
> show #!21 models
> hide #!21 models
> show #!22 models
> hide #!4 models
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\张叶/Desktop\movie10.mp4
Movie saved to C:\Users\张叶/Desktop\movie10.mp4
> hide #!22 models
> show #!4 models
> hide #7 models
> show #7 models
QWaitCondition: Destroyed while threads are still waiting
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.10rc202505070250 (2025-05-07)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 3.3.0 Core Profile Context 23.20.28.03.231124
OpenGL renderer: AMD Radeon(TM) Graphics
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: zh_CN.cp936
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows
Manufacturer: LENOVO
Model: 82SJ
OS: Microsoft Windows 11 家庭中文版 (Build 26100)
Memory: 14,702,026,752
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 6800HS Creator Edition
OSLanguage: zh-CN
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.3.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.3.2
build: 1.2.2.post1
certifi: 2025.4.26
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.3
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.5
ChimeraX-AtomicLibrary: 14.1.17
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.2.6
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10rc202505070250
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.1
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
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: 1.1.3
ChimeraX-ProfileGrids: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.10
contourpy: 1.3.2
coverage: 7.8.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.57.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.13.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.7
pluggy: 1.5.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.3.5
pytest-cov: 6.1.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pywin32: 310
pyzmq: 26.4.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.13.2
tzdata: 2025.2
urllib3: 2.4.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
WMI: 1.5.1
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Happened while setting HTML log text. Seems like the communication to the Chromium backend is sometimes an issue.