﻿id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
20007	Crash on Mac waking from sleep	chimerax-bug-report@…	Tom Goddard	"{{{
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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      __TEXT                      102f1c000-102f20000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX"",
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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
    ChimeraX-Segger: 1.0
    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
    ChimeraX-ViewDock: 1.5.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    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
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.4
    debugpy: 1.8.19
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.61.1
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    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
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.6.3
    jupyter_core: 5.9.1
    jupyterlab_widgets: 3.0.16
    kiwisolver: 1.4.9
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.3
    matplotlib: 3.10.7
    matplotlib-inline: 0.2.1
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.0
    ndindex: 1.10.1
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.14.1
    numpy: 1.26.4
    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
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.4.1
    psutil: 7.0.0
    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
}}}
"	defect	closed	normal		Window Toolkit		duplicate						all	ChimeraX
