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Opened 96 minutes ago
#20007 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-15.7.4-arm64-arm-64bit
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00000001f99e6240 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 414 in event_loop
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1064 in init
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.pdb_lib._load_libs, chimerax.surface._surface, PIL._imaging, psutil._psutil_osx, psutil._psutil_posix, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.chem_group._chem_group, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, lxml._elementpath, lxml.etree (total: 60)
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"procLaunch" : "2026-03-05 15:10:36.3750 -0600",
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"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
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"vmRegionInfo" : "0x8 is not in any region. Bytes before following region: 4344365048
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
__TEXT 102f1c000-102f20000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000008","rawCodes":[1,8],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000008"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":26938},
"vmregioninfo" : "0x8 is not in any region. Bytes before following region: 4344365048
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
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===== Log before crash start =====
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/jeffrey.ng/Downloads/7R03.cif format mmcif
7R03.cif title:
Neurofibromin occluded conformation [more info...]
Chain information for 7R03.cif #1
---
Chain | Description | UniProt
A B | Isoform I of Neurofibromin | NF1_HUMAN 1-2818
> open /Users/jeffrey.ng/Desktop/alphafold3/NF1_G848R_homo_dimer_model.cif
Chain information for NF1_G848R_homo_dimer_model.cif #2
---
Chain | Description
A B | .
Color NF1_G848R_homo_dimer_model.cif by residue attribute pLDDT_score
> matchmaker #2 to #1
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7R03.cif, chain A (#1) with NF1_G848R_homo_dimer_model.cif, chain B
(#2), sequence alignment score = 13143.2
RMSD between 289 pruned atom pairs is 1.403 angstroms; (across all 2241 pairs:
32.087)
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> matchmaker #2/B to #1/B
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 7R03.cif, chain B (#1) with NF1_G848R_homo_dimer_model.cif, chain B
(#2), sequence alignment score = 13105.4
RMSD between 250 pruned atom pairs is 1.398 angstroms; (across all 2246 pairs:
32.472)
> select 848
Expected an objects specifier or a keyword
> select :848
30 atoms, 26 bonds, 4 residues, 2 models selected
> hbonds sel showDist true
3 hydrogen bonds found
> hide atoms
> hide #!1 models
> show #!1 models
> show :848,1809,1738 stick
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #2 models
> show #2 models
> hide #!1 models
> select up
110 atoms, 104 bonds, 16 residues, 2 models selected
> select up
47470 atoms, 48426 bonds, 6006 residues, 2 models selected
> hbonds sel showDist true
7009 hydrogen bonds found
> show :848
> ui tool show "Selection Inspector"
> view :848
> show #!1 models
> style sel stick
Changed 47470 atom styles
> select 848
Expected an objects specifier or a keyword
> select :848
30 atoms, 26 bonds, 4 residues, 2 models selected
> show ~sel
> select up
110 atoms, 104 bonds, 16 residues, 2 models selected
> select down
30 atoms, 26 bonds, 4 residues, 2 models selected
> show !sel
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show sel only
> select :848
30 atoms, 26 bonds, 4 residues, 2 models selected
> select up
110 atoms, 104 bonds, 16 residues, 2 models selected
> show sel only
> close
> close session
> open /Users/jeffrey.ng/Desktop/alphafold3/NF1_G848R_homo_dimer_model.cif
> format mmcif
Chain information for NF1_G848R_homo_dimer_model.cif #1
---
Chain | Description
A B | .
Color NF1_G848R_homo_dimer_model.cif by residue attribute pLDDT_score
> open /Users/jeffrey.ng/Desktop/alphafold3/NF1_WT_homo_dimers_model.cif
Chain information for NF1_WT_homo_dimers_model.cif #2
---
Chain | Description
A B | .
Color NF1_WT_homo_dimers_model.cif by residue attribute pLDDT_score
> matchmaker #1 to #2
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker NF1_WT_homo_dimers_model.cif, chain A (#2) with
NF1_G848R_homo_dimer_model.cif, chain A (#1), sequence alignment score =
14365.4
RMSD between 1620 pruned atom pairs is 0.918 angstroms; (across all 2818
pairs: 11.673)
> select :848
30 atoms, 26 bonds, 4 residues, 2 models selected
> show ~sel
> show sel
> show sel only
> honds sel
Unknown command: honds sel
> hbonds sel
4 hydrogen bonds found
> select up
80 atoms, 76 bonds, 12 residues, 2 models selected
> hbonds sel showDist true
16 hydrogen bonds found
> close session
> open /Users/jeffrey.ng/Downloads/7R03.cif format mmcif
7R03.cif title:
Neurofibromin occluded conformation [more info...]
Chain information for 7R03.cif #1
---
Chain | Description | UniProt
A B | Isoform I of Neurofibromin | NF1_HUMAN 1-2818
Unsupported scale factor (0.000000) detected on Display0
> swapaa 848 R
Missing or invalid "residues" argument: invalid residues specifier
> swapaa :848 R
Using Dunbrack library
/A GLY 848: phi -64.2, psi -43.3 trans
Dunbrack rotamer library does not support R
> swapaa :848 seq:R
Using Dunbrack library
/A GLY 848: phi -64.2, psi -43.3 trans
/B GLY 848: phi -63.6, psi -34.5 trans
Applying ARG rotamer (chi angles: -68.6 -73.6 -68.1 108.8) to /A ARG 848
Applying ARG rotamer (chi angles: -70.5 176.7 63.4 84.8) to /B ARG 848
> close session
> open /Users/jeffrey.ng/Desktop/alphafold3/7R04.cif format mmcif
7R04.cif title:
Neurofibromin in open conformation [more info...]
Chain information for 7R04.cif #1
---
Chain | Description | UniProt
A B | Isoform I of Neurofibromin | NF1_HUMAN 1-2818
Non-standard residues in 7R04.cif #1
---
GSP — 5'-guanosine-diphosphate-monothiophosphate
2176 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> open /Users/jeffrey.ng/Desktop/alphafold3/7R04.cif
7R04.cif title:
Neurofibromin in open conformation [more info...]
Chain information for 7R04.cif #2
---
Chain | Description | UniProt
A B | Isoform I of Neurofibromin | NF1_HUMAN 1-2818
Non-standard residues in 7R04.cif #2
---
GSP — 5'-guanosine-diphosphate-monothiophosphate
2176 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> close session
> open /Users/jeffrey.ng/Desktop/alphafold3/7R04.cif format mmcif
7R04.cif title:
Neurofibromin in open conformation [more info...]
Chain information for 7R04.cif #1
---
Chain | Description | UniProt
A B | Isoform I of Neurofibromin | NF1_HUMAN 1-2818
Non-standard residues in 7R04.cif #1
---
GSP — 5'-guanosine-diphosphate-monothiophosphate
2176 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> swapaa :848 seq:R
Using Dunbrack library
/A GLY 848: phi -63.5, psi -17.0 trans
/B GLY 848: phi -74.8, psi -2.1 trans
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /B MET 1225 SD
Applying ARG rotamer (chi angles: -178.4 -93.5 178.0 -84.4) to /A ARG 848
Applying ARG rotamer (chi angles: -177.9 -93.5 178.4 -84.8) to /B ARG 848
> open /Users/jeffrey.ng/Desktop/alphafold3/7R04.cif
7R04.cif title:
Neurofibromin in open conformation [more info...]
Chain information for 7R04.cif #2
---
Chain | Description | UniProt
A B | Isoform I of Neurofibromin | NF1_HUMAN 1-2818
Non-standard residues in 7R04.cif #2
---
GSP — 5'-guanosine-diphosphate-monothiophosphate
2176 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> matchmaker #1 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 7R04.cif, chain A (#2) with 7R04.cif, chain A (#1), sequence
alignment score = 13948.4
RMSD between 2326 pruned atom pairs is 0.000 angstroms; (across all 2326
pairs: 0.000)
> close session
> open /Users/jeffrey.ng/Downloads/7R03.cif format mmcif
7R03.cif title:
Neurofibromin occluded conformation [more info...]
Chain information for 7R03.cif #1
---
Chain | Description | UniProt
A B | Isoform I of Neurofibromin | NF1_HUMAN 1-2818
Unsupported scale factor (0.000000) detected on Display0
> open /Users/jeffrey.ng/Desktop/alphafold3/NF1_G848R_homo_dimer_model.cif
Chain information for NF1_G848R_homo_dimer_model.cif #2
---
Chain | Description
A B | .
Color NF1_G848R_homo_dimer_model.cif by residue attribute pLDDT_score
> matchmaker #2/B to #1/B
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7R03.cif, chain B (#1) with NF1_G848R_homo_dimer_model.cif, chain B
(#2), sequence alignment score = 13105.4
RMSD between 250 pruned atom pairs is 1.398 angstroms; (across all 2246 pairs:
32.472)
> select ~sel & ##selected
Nothing selected
> matchmaker #2/B to #1/B showrmsd true
Expected a keyword
> matchmaker #2/B to #1/B showRmsd true
Expected a keyword
> matchmaker #2 to #1 showRmsd true
Expected a keyword
> matchmaker #2 to #1 showRmsd true #2
Expected a keyword
> 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 7R03.cif, chain A (#1) with NF1_G848R_homo_dimer_model.cif, chain B
(#2), sequence alignment score = 13143.2
RMSD between 289 pruned atom pairs is 1.403 angstroms; (across all 2241 pairs:
32.087)
> hbonds :848
0 hydrogen bonds found
> matchmaker #2/B to #1/B
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 7R03.cif, chain B (#1) with NF1_G848R_homo_dimer_model.cif, chain B
(#2), sequence alignment score = 13105.4
RMSD between 250 pruned atom pairs is 1.398 angstroms; (across all 2246 pairs:
32.472)
> hbonds :848
3 hydrogen bonds found
> setattr #2 residues logAttribute seq_rmsd log true
Expected a keyword
> setattr #2 residues logAttribute seq_rmsd
Assigning logAttribute attribute to 5636 items
Not creating attribute 'logAttribute'; use 'create true' to override
Unsupported scale factor (0.000000) detected on Display0
> open /Users/jeffrey.ng/Desktop/alphafold3/nf1_wt_G848R_hetrodimer.cxs
> view name session-start
opened ChimeraX session
> close session
> open /Users/jeffrey.ng/Downloads/7R03.cif format mmcif
7R03.cif title:
Neurofibromin occluded conformation [more info...]
Chain information for 7R03.cif #1
---
Chain | Description | UniProt
A B | Isoform I of Neurofibromin | NF1_HUMAN 1-2818
> open /Users/jeffrey.ng/Desktop/alphafold3/NF1_G848R_homo_dimer_model.cif
Chain information for NF1_G848R_homo_dimer_model.cif #2
---
Chain | Description
A B | .
Color NF1_G848R_homo_dimer_model.cif by residue attribute pLDDT_score
> matchmaker #2/B to #1/B
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7R03.cif, chain B (#1) with NF1_G848R_homo_dimer_model.cif, chain B
(#2), sequence alignment score = 13105.4
RMSD between 250 pruned atom pairs is 1.398 angstroms; (across all 2246 pairs:
32.472)
> save /Users/jeffrey.ng/Desktop/testsave.txt attr seq_rmsd selectedOnly false
> models #2
No known data format for file suffix '.txt'
> setattr #2 residues logAttribute seq_rmsd log true
Expected a keyword
> setattr #2 residues logAttribute seq_rmsd
Assigning logAttribute attribute to 5636 items
Not creating attribute 'logAttribute'; use 'create true' to override
> log save testme.txt
> ui tool show "Render/Select by Attribute"
'Attribute name' field is blank
> setattr log true
Missing or invalid "attrValue" argument: Expected a text string
> setattr residues seq_rmsd log true
Expected a keyword
> setattr residues seq_rmsd
Missing or invalid "attrValue" argument: Expected a text string
> setattr #2 residues seq_rmsd
Missing or invalid "attrValue" argument: Expected a text string
> setattr #2 residues seq_rmsd log tue
Expected a keyword
> setattr #2 residues seq_rmsd log rue
Expected a keyword
> log save /Users/jeffrey.ng/Desktop/NF1_scores.txt
> save /Users/jeffrey.ng/Desktop/NF1_rmsd.def attr seq_rmsd models #2
No known data format for file suffix '.def'
> save /Users/jeffrey.ng/Desktop/NF1_rmsd.txt seq_rmsd models #2
No known data format for file suffix '.txt'
> matchmaker #2/B to #1/B showAlignment true
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 7R03.cif, chain B (#1) with NF1_G848R_homo_dimer_model.cif, chain B
(#2), sequence alignment score = 13105.4
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 7R03.cif #1/B,
NF1_G848R_homo_dimer_model.cif #2/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 250 pruned atom pairs is 1.398 angstroms; (across all 2246 pairs:
32.472)
> save /Users/jeffrey.ng/Desktop/NF1_rmsd.txt attr seq_rmsd models #2
No known data format for file suffix '.txt'
> sequence header rmsd save browse
> close
> close session
> open /Users/jeffrey.ng/Downloads/7R03.cif format mmcif
7R03.cif title:
Neurofibromin occluded conformation [more info...]
Chain information for 7R03.cif #1
---
Chain | Description | UniProt
A B | Isoform I of Neurofibromin | NF1_HUMAN 1-2818
> open /Users/jeffrey.ng/Desktop/alphafold3/NF1_WT_G848R_dimer_model.cif
Chain information for NF1_WT_G848R_dimer_model.cif #2
---
Chain | Description
A | .
B | .
Color NF1_WT_G848R_dimer_model.cif by residue attribute pLDDT_score
> matchmaker #2/B to #1/B showAlignment true
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7R03.cif, chain B (#1) with NF1_WT_G848R_dimer_model.cif, chain B
(#2), sequence alignment score = 13068.8
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 7R03.cif #1/B,
NF1_WT_G848R_dimer_model.cif #2/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 442 pruned atom pairs is 1.103 angstroms; (across all 2246 pairs:
29.421)
> sequence header rmsd save browse
> close session
> open /Users/jeffrey.ng/Downloads/7R03.cif format mmcif
7R03.cif title:
Neurofibromin occluded conformation [more info...]
Chain information for 7R03.cif #1
---
Chain | Description | UniProt
A B | Isoform I of Neurofibromin | NF1_HUMAN 1-2818
> open /Users/jeffrey.ng/Desktop/alphafold3/R1809C_homo_dimer_model.cif
Chain information for R1809C_homo_dimer_model.cif #2
---
Chain | Description
A B | .
Color R1809C_homo_dimer_model.cif by residue attribute pLDDT_score
> matchmaker #2/B to #1/B showAlignment true
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7R03.cif, chain B (#1) with R1809C_homo_dimer_model.cif, chain B
(#2), sequence alignment score = 13082
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 7R03.cif #1/B,
R1809C_homo_dimer_model.cif #2/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 311 pruned atom pairs is 0.904 angstroms; (across all 2246 pairs:
30.845)
> sequence header rmsd save browse
> close session
> open /Users/jeffrey.ng/Downloads/7R03.cif format mmcif
7R03.cif title:
Neurofibromin occluded conformation [more info...]
Chain information for 7R03.cif #1
---
Chain | Description | UniProt
A B | Isoform I of Neurofibromin | NF1_HUMAN 1-2818
> open /Users/jeffrey.ng/Desktop/alphafold3/NF1_WT_R1809C_dimer_model.cif
Chain information for NF1_WT_R1809C_dimer_model.cif #2
---
Chain | Description
A | .
B | .
Color NF1_WT_R1809C_dimer_model.cif by residue attribute pLDDT_score
> matchmaker #2/B to #1/B showAlignment true
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7R03.cif, chain B (#1) with NF1_WT_R1809C_dimer_model.cif, chain B
(#2), sequence alignment score = 13062.2
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 7R03.cif #1/B,
NF1_WT_R1809C_dimer_model.cif #2/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 534 pruned atom pairs is 1.134 angstroms; (across all 2246 pairs:
27.908)
> sequence header rmsd save browse
> close session
> open /Users/jeffrey.ng/Desktop/alphafold3/7R04.cif format mmcif
7R04.cif title:
Neurofibromin in open conformation [more info...]
Chain information for 7R04.cif #1
---
Chain | Description | UniProt
A B | Isoform I of Neurofibromin | NF1_HUMAN 1-2818
Non-standard residues in 7R04.cif #1
---
GSP — 5'-guanosine-diphosphate-monothiophosphate
2176 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> open /Users/jeffrey.ng/Desktop/alphafold3/R1809C_homo_dimer_model.cif
Chain information for R1809C_homo_dimer_model.cif #2
---
Chain | Description
A B | .
Color R1809C_homo_dimer_model.cif by residue attribute pLDDT_score
> matchmaker #2/B to #1/B showAlignment true
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7R04.cif, chain B (#1) with R1809C_homo_dimer_model.cif, chain B
(#2), sequence alignment score = 13005.8
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 7R04.cif #1/B,
R1809C_homo_dimer_model.cif #2/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 323 pruned atom pairs is 0.939 angstroms; (across all 2229 pairs:
24.703)
> sequence header rmsd save browse
> close session
> open /Users/jeffrey.ng/Desktop/alphafold3/7R04.cif format mmcif
7R04.cif title:
Neurofibromin in open conformation [more info...]
Chain information for 7R04.cif #1
---
Chain | Description | UniProt
A B | Isoform I of Neurofibromin | NF1_HUMAN 1-2818
Non-standard residues in 7R04.cif #1
---
GSP — 5'-guanosine-diphosphate-monothiophosphate
2176 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> open /Users/jeffrey.ng/Desktop/alphafold3/NF1_G848R_homo_dimer_model.cif
Chain information for NF1_G848R_homo_dimer_model.cif #2
---
Chain | Description
A B | .
Color NF1_G848R_homo_dimer_model.cif by residue attribute pLDDT_score
> matchmaker #2/B to #1/B showAlignment true
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7R04.cif, chain B (#1) with NF1_G848R_homo_dimer_model.cif, chain B
(#2), sequence alignment score = 13019.6
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 7R04.cif #1/B,
NF1_G848R_homo_dimer_model.cif #2/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 298 pruned atom pairs is 1.222 angstroms; (across all 2229 pairs:
22.486)
> sequence header rmsd save browse
> close session
> open /Users/jeffrey.ng/Desktop/alphafold3/7R04.cif format mmcif
7R04.cif title:
Neurofibromin in open conformation [more info...]
Chain information for 7R04.cif #1
---
Chain | Description | UniProt
A B | Isoform I of Neurofibromin | NF1_HUMAN 1-2818
Non-standard residues in 7R04.cif #1
---
GSP — 5'-guanosine-diphosphate-monothiophosphate
2176 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> open /Users/jeffrey.ng/Desktop/alphafold3/NF1_WT_R1809C_dimer_model.cif
Chain information for NF1_WT_R1809C_dimer_model.cif #2
---
Chain | Description
A | .
B | .
Color NF1_WT_R1809C_dimer_model.cif by residue attribute pLDDT_score
> matchmaker #2/B to #1/B showAlignment true
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7R04.cif, chain B (#1) with NF1_WT_R1809C_dimer_model.cif, chain B
(#2), sequence alignment score = 12991.4
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 7R04.cif #1/B,
NF1_WT_R1809C_dimer_model.cif #2/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 421 pruned atom pairs is 1.347 angstroms; (across all 2229 pairs:
21.555)
> sequence header rmsd save browse
> close session
> open /Users/jeffrey.ng/Desktop/alphafold3/7R04.cif format mmcif
7R04.cif title:
Neurofibromin in open conformation [more info...]
Chain information for 7R04.cif #1
---
Chain | Description | UniProt
A B | Isoform I of Neurofibromin | NF1_HUMAN 1-2818
Non-standard residues in 7R04.cif #1
---
GSP — 5'-guanosine-diphosphate-monothiophosphate
2176 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> open /Users/jeffrey.ng/Desktop/alphafold3/NF1_WT_G848R_dimer_model.cif
Chain information for NF1_WT_G848R_dimer_model.cif #2
---
Chain | Description
A | .
B | .
Color NF1_WT_G848R_dimer_model.cif by residue attribute pLDDT_score
> matchmaker #2/B to #1/B showAlignment true
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7R04.cif, chain B (#1) with NF1_WT_G848R_dimer_model.cif, chain B
(#2), sequence alignment score = 13005.2
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 7R04.cif #1/B,
NF1_WT_G848R_dimer_model.cif #2/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 380 pruned atom pairs is 1.355 angstroms; (across all 2229 pairs:
22.464)
> sequence header rmsd save browse
> close session
> open /Users/jeffrey.ng/Downloads/7R03.cif format mmcif
7R03.cif title:
Neurofibromin occluded conformation [more info...]
Chain information for 7R03.cif #1
---
Chain | Description | UniProt
A B | Isoform I of Neurofibromin | NF1_HUMAN 1-2818
> swapaa 848 seq R
Missing or invalid "residues" argument: invalid residues specifier
> swapaa :848 arg
Using Dunbrack library
/A GLY 848: phi -64.2, psi -43.3 trans
/B GLY 848: phi -63.6, psi -34.5 trans
Applying ARG rotamer (chi angles: -68.6 -73.6 -68.1 108.8) to /A ARG 848
Applying ARG rotamer (chi angles: -70.5 176.7 63.4 84.8) to /B ARG 848
> open /Users/jeffrey.ng/Desktop/alphafold3/NF1_WT_homo_dimers_model.cif
Chain information for NF1_WT_homo_dimers_model.cif #2
---
Chain | Description
A B | .
Color NF1_WT_homo_dimers_model.cif by residue attribute pLDDT_score
> matchmaker #1/B to #2/B
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker NF1_WT_homo_dimers_model.cif, chain B (#2) with 7R03.cif, chain B
(#1), sequence alignment score = 13097
RMSD between 381 pruned atom pairs is 0.908 angstroms; (across all 2246 pairs:
30.255)
> matchmaker #1/B to #2/B showAlignment true
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 NF1_WT_homo_dimers_model.cif, chain B (#2) with 7R03.cif, chain B
(#1), sequence alignment score = 13097
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 7R03.cif #1/B,
NF1_WT_homo_dimers_model.cif #2/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 381 pruned atom pairs is 0.908 angstroms; (across all 2246 pairs:
30.255)
> sequence header rmsd save browse
> close session
> open /Users/jeffrey.ng/Downloads/7R03.cif format mmcif
7R03.cif title:
Neurofibromin occluded conformation [more info...]
Chain information for 7R03.cif #1
---
Chain | Description | UniProt
A B | Isoform I of Neurofibromin | NF1_HUMAN 1-2818
> swapaa #1/B:848 arg
Using Dunbrack library
/B GLY 848: phi -63.6, psi -34.5 trans
Applying ARG rotamer (chi angles: -70.5 176.7 63.4 84.8) to /B ARG 848
> open /Users/jeffrey.ng/Desktop/alphafold3/NF1_WT_homo_dimers_model.cif
Chain information for NF1_WT_homo_dimers_model.cif #2
---
Chain | Description
A B | .
Color NF1_WT_homo_dimers_model.cif by residue attribute pLDDT_score
> matchmaker #1/B to #2/B showAlignment true
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker NF1_WT_homo_dimers_model.cif, chain B (#2) with 7R03.cif, chain B
(#1), sequence alignment score = 13097
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 7R03.cif #1/B,
NF1_WT_homo_dimers_model.cif #2/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 381 pruned atom pairs is 0.908 angstroms; (across all 2246 pairs:
30.255)
> sequence header rmsd save browse
> close session
> open /Users/jeffrey.ng/Downloads/7R03.cif format mmcif
7R03.cif title:
Neurofibromin occluded conformation [more info...]
Chain information for 7R03.cif #1
---
Chain | Description | UniProt
A B | Isoform I of Neurofibromin | NF1_HUMAN 1-2818
> swapaa #1/B:1809 cys
Using Dunbrack library
/B ARG 1809: phi -65.2, psi -48.0 trans
Applying CYS rotamer (chi angles: -69.1) to /B CYS 1809
> open /Users/jeffrey.ng/Desktop/alphafold3/NF1_WT_homo_dimers_model.cif
Chain information for NF1_WT_homo_dimers_model.cif #2
---
Chain | Description
A B | .
Color NF1_WT_homo_dimers_model.cif by residue attribute pLDDT_score
> matchmaker #1/B to #2/B showAlignment true
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker NF1_WT_homo_dimers_model.cif, chain B (#2) with 7R03.cif, chain B
(#1), sequence alignment score = 13097
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 7R03.cif #1/B,
NF1_WT_homo_dimers_model.cif #2/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 381 pruned atom pairs is 0.908 angstroms; (across all 2246 pairs:
30.255)
> sequence header rmsd save browse
> swapaa #1:1809 cys
Using Dunbrack library
7R03.cif #1/A ARG 1809: phi -65.1, psi -46.4 trans
7R03.cif #1/B CYS 1809: phi -65.2, psi -48.0 trans
Applying CYS rotamer (chi angles: -69.1) to 7R03.cif #1/A CYS 1809
Applying CYS rotamer (chi angles: -69.1) to 7R03.cif #1/B CYS 1809
> matchmaker #1/B to #2/B showAlignment true
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 NF1_WT_homo_dimers_model.cif, chain B (#2) with 7R03.cif, chain B
(#1), sequence alignment score = 13097
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: 7R03.cif #1/B,
NF1_WT_homo_dimers_model.cif #2/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 381 pruned atom pairs is 0.908 angstroms; (across all 2246 pairs:
30.255)
> sequence header 2 rmsd save browse
> close session
> open /Users/jeffrey.ng/Desktop/alphafold3/7R04.cif format mmcif
7R04.cif title:
Neurofibromin in open conformation [more info...]
Chain information for 7R04.cif #1
---
Chain | Description | UniProt
A B | Isoform I of Neurofibromin | NF1_HUMAN 1-2818
Non-standard residues in 7R04.cif #1
---
GSP — 5'-guanosine-diphosphate-monothiophosphate
2176 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> open /Users/jeffrey.ng/Desktop/alphafold3/NF1_WT_homo_dimers_model.cif
Chain information for NF1_WT_homo_dimers_model.cif #2
---
Chain | Description
A B | .
Color NF1_WT_homo_dimers_model.cif by residue attribute pLDDT_score
> swapaa #1/B:848 arg
Using Dunbrack library
7R04.cif #1/B GLY 848: phi -74.8, psi -2.1 trans
Applying ARG rotamer (chi angles: -177.9 -93.5 178.4 -84.8) to 7R04.cif #1/B
ARG 848
> matchmaker #1/B to #2/B showAlignment true
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker NF1_WT_homo_dimers_model.cif, chain B (#2) with 7R04.cif, chain B
(#1), sequence alignment score = 13031
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 7R04.cif #1/B,
NF1_WT_homo_dimers_model.cif #2/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 456 pruned atom pairs is 1.007 angstroms; (across all 2229 pairs:
22.075)
> sequence header rmsd save browse
> swapaa #1:848 arg
Using Dunbrack library
7R04.cif #1/A GLY 848: phi -63.5, psi -17.0 trans
7R04.cif #1/B ARG 848: phi -74.8, psi -2.1 trans
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 7R04.cif #1/B MET 1225 SD
Applying ARG rotamer (chi angles: -70.0 178.2 -180.0 173.1) to 7R04.cif #1/A
ARG 848
Applying ARG rotamer (chi angles: -68.0 179.0 -179.9 176.5) to 7R04.cif #1/B
ARG 848
> matchmaker #1/B to #2/B showAlignment true
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 NF1_WT_homo_dimers_model.cif, chain B (#2) with 7R04.cif, chain B
(#1), sequence alignment score = 13031
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: 7R04.cif #1/B,
NF1_WT_homo_dimers_model.cif #2/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 456 pruned atom pairs is 1.007 angstroms; (across all 2229 pairs:
22.075)
> sequence header 2 rmsd save browse
> close session
> open /Users/jeffrey.ng/Desktop/alphafold3/7R04.cif format mmcif
7R04.cif title:
Neurofibromin in open conformation [more info...]
Chain information for 7R04.cif #1
---
Chain | Description | UniProt
A B | Isoform I of Neurofibromin | NF1_HUMAN 1-2818
Non-standard residues in 7R04.cif #1
---
GSP — 5'-guanosine-diphosphate-monothiophosphate
2176 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> swapaa #1/B:1809 cys
Using Dunbrack library
/B ARG 1809: phi -70.9, psi -37.0 trans
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /B MET 1225 SD
Applying CYS rotamer (chi angles: -69.5) to /B CYS 1809
> open /Users/jeffrey.ng/Desktop/alphafold3/NF1_WT_homo_dimers_model.cif
Chain information for NF1_WT_homo_dimers_model.cif #2
---
Chain | Description
A B | .
Color NF1_WT_homo_dimers_model.cif by residue attribute pLDDT_score
> matchmaker #1/B to #2/B showAlignment true
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker NF1_WT_homo_dimers_model.cif, chain B (#2) with 7R04.cif, chain B
(#1), sequence alignment score = 13031
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 7R04.cif #1/B,
NF1_WT_homo_dimers_model.cif #2/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 456 pruned atom pairs is 1.007 angstroms; (across all 2229 pairs:
22.075)
> sequence header rmsd save browse
> swapaa #1:1809 cys
Using Dunbrack library
7R04.cif #1/A ARG 1809: phi -75.2, psi -26.3 trans
7R04.cif #1/B CYS 1809: phi -70.9, psi -37.0 trans
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 7R04.cif #1/B MET 1225 SD
Applying CYS rotamer (chi angles: -68.1) to 7R04.cif #1/A CYS 1809
Applying CYS rotamer (chi angles: -69.5) to 7R04.cif #1/B CYS 1809
> matchmaker #1/B to #2/B showAlignment true
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 NF1_WT_homo_dimers_model.cif, chain B (#2) with 7R04.cif, chain B
(#1), sequence alignment score = 13031
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: 7R04.cif #1/B,
NF1_WT_homo_dimers_model.cif #2/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 456 pruned atom pairs is 1.007 angstroms; (across all 2229 pairs:
22.075)
> sequence header 2 rmsd save browse
Unsupported scale factor (0.000000) detected on Display0
> close sessioin
Expected a models specifier or a keyword
> close session
> open /Users/jeffrey.ng/Downloads/7R03.cif format mmcif
7R03.cif title:
Neurofibromin occluded conformation [more info...]
Chain information for 7R03.cif #1
---
Chain | Description | UniProt
A B | Isoform I of Neurofibromin | NF1_HUMAN 1-2818
> swapaa :848 Arg
Using Dunbrack library
/A GLY 848: phi -64.2, psi -43.3 trans
/B GLY 848: phi -63.6, psi -34.5 trans
Applying ARG rotamer (chi angles: -68.6 -73.6 -68.1 108.8) to /A ARG 848
Applying ARG rotamer (chi angles: -70.5 176.7 63.4 84.8) to /B ARG 848
> open /Users/jeffrey.ng/Downloads/7R03.cif
7R03.cif title:
Neurofibromin occluded conformation [more info...]
Chain information for 7R03.cif #2
---
Chain | Description | UniProt
A B | Isoform I of Neurofibromin | NF1_HUMAN 1-2818
> matchmaker #1 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 7R03.cif, chain B (#2) with 7R03.cif, chain B (#1), sequence
alignment score = 13793.6
RMSD between 2246 pruned atom pairs is 0.000 angstroms; (across all 2246
pairs: 0.000)
> matchmaker #1 to #2 showAlignment true
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 7R03.cif, chain B (#2) with 7R03.cif, chain B (#1), sequence
alignment score = 13793.6
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 7R03.cif #1/B, 7R03.cif #2/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 2246 pruned atom pairs is 0.000 angstroms; (across all 2246
pairs: 0.000)
> sequence header rmsd save browse
Command cancelled by user
===== Log before crash end =====
Log:
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M3 Max
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,11
Model Number: Z1AH000V9LL/A
Chip: Apple M3 Max
Total Number of Cores: 14 (10 performance and 4 efficiency)
Memory: 36 GB
System Firmware Version: 13822.81.10
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.7.4 (24G517)
Kernel Version: Darwin 24.6.0
Time since boot: 16 days, 10 hours, 2 minutes
Graphics/Displays:
Apple M3 Max:
Chipset Model: Apple M3 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 30
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
DELL U3415W:
Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
UI Looks like: 3440 x 1440 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.1
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.12
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
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ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
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ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.1
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fonttools: 4.61.1
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glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
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jsonschema-specifications: 2025.9.1
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Markdown: 3.8.2
MarkupSafe: 3.0.3
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mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
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OpenMM: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
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ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
roman-numerals-py: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
sse-starlette: 3.2.0
stack-data: 0.6.3
starlette: 0.52.1
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
urllib3: 2.6.3
uvicorn: 0.40.0
wcwidth: 0.3.2
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
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