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Opened 2 years ago
Closed 2 years ago
#9858 closed defect (can't reproduce)
Crash processing atomic changes data
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-6.1.0-5-amd64-x86_64-with-glibc2.37
ChimeraX Version: 1.7.dev202307110732 (2023-07-11 07:32:07 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 0x00007fbae0859740 (most recent call first):
Garbage-collecting
File "/slow_data/bioinfo_apps/opt/chimerax-2023.07.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 2194 in process_changes
File "/slow_data/bioinfo_apps/opt/chimerax-2023.07.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 2200 in changes
File "/slow_data/bioinfo_apps/opt/chimerax-2023.07.11/lib/python3.11/site-packages/chimerax/atomic/changes.py", line 25 in check_for_changes
File "/slow_data/bioinfo_apps/opt/chimerax-2023.07.11/lib/python3.11/site-packages/chimerax/atomic/__init__.py", line 66 in
File "/slow_data/bioinfo_apps/opt/chimerax-2023.07.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 138 in invoke
File "/slow_data/bioinfo_apps/opt/chimerax-2023.07.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 237 in _activate
File "/slow_data/bioinfo_apps/opt/chimerax-2023.07.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 206 in activate
File "/slow_data/bioinfo_apps/opt/chimerax-2023.07.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 382 in activate_trigger
File "/slow_data/bioinfo_apps/opt/chimerax-2023.07.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2994 in command_trigger
File "/slow_data/bioinfo_apps/opt/chimerax-2023.07.11/lib/python3.11/contextlib.py", line 144 in __exit__
File "/slow_data/bioinfo_apps/opt/chimerax-2023.07.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2888 in run
File "/slow_data/bioinfo_apps/opt/chimerax-2023.07.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
File "/slow_data/bioinfo_apps/opt/chimerax-2023.07.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
File "/slow_data/bioinfo_apps/opt/chimerax-2023.07.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/slow_data/bioinfo_apps/opt/chimerax-2023.07.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 893 in init
File "/slow_data/bioinfo_apps/opt/chimerax-2023.07.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1044 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.surface._surface, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, 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, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, lxml._elementpath, lxml.etree, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 62)
===== Log before crash start =====
UCSF ChimeraX version: 1.7.dev202307110732 (2023-07-11)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open B5XAZ0 fromDatabase alphafold
Summary of feedback from opening B5XAZ0 fetched from alphafold
---
note | Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json
Chain information for AlphaFold B5XAZ0 #1
---
Chain | Description | UniProt
A | Angiogenin-1 | B5XAZ0_SALSA 1-145
Color AlphaFold B5XAZ0 by residue attribute pLDDT_score
> open 1ANG fromDatabase uniprot
Invalid UniProt entry name / accession number: 1ANG
> close all
> open 1ang fromDatabase pdb
1ang title:
Crystal structure of human angiogenin reveals the structural basis for its
functional divergence from ribonuclease [more info...]
Chain information for 1ang #1
---
Chain | Description | UniProt
A | ANGIOGENIN | ANGI_HUMAN 1-123
1ang mmCIF Assemblies
---
1| author_defined_assembly
> open 7bfk fromDatabase pdb
7bfk title:
X-ray structure of SS-RNase-2 [more info...]
Chain information for 7bfk #2
---
Chain | Description | UniProt
A B | Angiogenin-1 | B5XAZ0_SALSA 1-126
7bfk mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> delete /b
> mmaker #1 to #2 show 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 7bfk, chain A (#2) with 1ang, chain A (#1), sequence alignment
score = 236.6
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: 1ang #1/A, 7bfk #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 86 pruned atom pairs is 0.827 angstroms; (across all 115 pairs:
3.945)
> select #2/A:3-17,22-28,39-58,60-64,68-84,90-107,109-112
> #1/A:3-17,25-31,39-58,61-65,69-85,91-108,110-113
1346 atoms, 1366 bonds, 172 residues, 2 models selected
> select #2/A:40
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:40 #1/A:40
18 atoms, 16 bonds, 2 residues, 2 models selected
MatchMaker Alignment [ID: 1] region 7bfk, chain A..1ang, chain A [44] RMSD:
0.286
> select #2/A:13
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:13 #1/A:13
20 atoms, 20 bonds, 2 residues, 2 models selected
MatchMaker Alignment [ID: 1] region 7bfk, chain A..1ang, chain A [14] RMSD:
0.561
> select #2/A:113
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:113 #1/A:114
20 atoms, 20 bonds, 2 residues, 2 models selected
MatchMaker Alignment [ID: 1] region 7bfk, chain A..1ang, chain A [118] RMSD:
2.649
> select #2/A:113 #1/A:114
20 atoms, 20 bonds, 2 residues, 2 models selected
MatchMaker Alignment [ID: 1] region 7bfk, chain A..1ang, chain A [118] RMSD:
2.649
> select #2/A:113 #1/A:40,114
29 atoms, 28 bonds, 3 residues, 2 models selected
MatchMaker Alignment [ID: 1] region 7bfk, chain A..1ang, chain A [118] + 1
other block RMSD: 2.649
> select #2/A:113 #1/A:40,114
29 atoms, 28 bonds, 3 residues, 2 models selected
MatchMaker Alignment [ID: 1] region 7bfk, chain A..1ang, chain A [118] + 1
other block RMSD: 2.649
> select #2/A:113 #1/A:40,114
29 atoms, 28 bonds, 3 residues, 2 models selected
MatchMaker Alignment [ID: 1] region 7bfk, chain A..1ang, chain A [118] + 1
other block RMSD: 2.649
> select #2/A:40 #1/A:40
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #2/A:40 #1/A:40
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #2/A:40 #1/A:40
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #2/A:13 #1/A:13
20 atoms, 20 bonds, 2 residues, 2 models selected
> select #1/A:13 #2/A:13
20 atoms, 20 bonds, 2 residues, 2 models selected
> color gray
> select #1:13,40,113 | #2:13,14,114
55 atoms, 53 bonds, 6 residues, 2 models selected
> select #1:13,40,114 | #2:13,14,113
56 atoms, 55 bonds, 6 residues, 2 models selected
> select #1:13,40,114 | #2:13,40,113
58 atoms, 56 bonds, 6 residues, 2 models selected
> display sel
> preset licorice
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> select #1:13,40,114 | #2:13,40,113
58 atoms, 56 bonds, 6 residues, 2 models selected
> display sel
> ~select
Nothing selected
> color bymodel
> open
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
Chain information for
rnaselike_DM_50091_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #3
---
Chain | Description
A | No description available
> preset licorice
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> mmaker #3 to #2 show 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 7bfk, chain A (#2) with
rnaselike_DM_50091_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain
A (#3), sequence alignment score = 268.1
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: 7bfk #2/A,
rnaselike_DM_50091_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #3/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 84 pruned atom pairs is 0.831 angstroms; (across all 115 pairs:
4.143)
> select #3:12,39,110
56 atoms, 55 bonds, 3 residues, 1 model selected
> select #1:13,40,114 | #2:13,40,113 | #3:12,39,110
114 atoms, 111 bonds, 9 residues, 3 models selected
> display sel
> save
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/1ang_7bfk_dm_afold_mmaker_HKH.cxs
> open B5XAZ0 fromDatabase alphafold
Chain information for AlphaFold B5XAZ0 #4
---
Chain | Description | UniProt
A | Angiogenin-1 | B5XAZ0_SALSA 1-145
Color AlphaFold B5XAZ0 by residue attribute pLDDT_score
Associated AlphaFold B5XAZ0 chain A to 7bfk, chain A with 1 mismatch
Chains used in RMSD evaluation for alignment 1: 1ang #1/A, 7bfk #2/A,
AlphaFold B5XAZ0 #4/A
Associated AlphaFold B5XAZ0 chain A to 7bfk, chain A with 1 mismatch
Chains used in RMSD evaluation for alignment 2: 7bfk #2/A,
rnaselike_DM_50091_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #3/A,
AlphaFold B5XAZ0 #4/A
> mmaker #4 to #7
No 'to' model specified
> mmaker #4 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 7bfk, chain A (#2) with AlphaFold B5XAZ0, chain A (#4), sequence
alignment score = 580.2
RMSD between 97 pruned atom pairs is 0.687 angstroms; (across all 125 pairs:
4.636)
> preset licorice
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> color bymodel
> hide #3 models
> show #3 models
> hide #1 models
> hide #3 models
> show #1 models
> hide #2 models
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> preset licorice
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> hide #4 models
> show #4 models
> show #3 models
> hide #1 models
> show #1 models
> show #2 models
> hide #1 models
> hide #4 models
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> select #1:13,40,114 | #2:13,40,113 | #3:12,39,110
114 atoms, 111 bonds, 9 residues, 3 models selected
> close #4
Chains used in RMSD evaluation for alignment 1: 1ang #1/A, 7bfk #2/A
Chains used in RMSD evaluation for alignment 2: 7bfk #2/A,
rnaselike_DM_50091_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #3/A
> show #1 models
> close all
> open
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/1ang_7bfk_dm_afold_mmaker_HKH.cxs
opened ChimeraX session
> coulombic sel
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
7bfk #2/A ASN 66 ND2
7bfk #2/A ASN 66 OD1
7bfk #2/A ASN 66 CG
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 1ang_A SES surface #1.1: minimum, -8.04, mean 3.52,
maximum 19.83
Coulombic values for 7bfk_A SES surface #2.1: minimum, -23.67, mean 0.33,
maximum 14.40
Coulombic values for
rnaselike_DM_50091_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb_A SES
surface #3.1: minimum, -15.14, mean -0.74, maximum 10.53
To also show corresponding color key, enter the above coulombic command and
add key true
> tile
3 models tiled
Chains used in RMSD evaluation for alignment 1: 1ang #1/A, 7bfk #2/A
Chains used in RMSD evaluation for alignment 2: 7bfk #2/A,
rnaselike_DM_50091_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #3/A
> ui windowfill toggle
> tile
3 models tiled
> tile ncol 3
Expected a models specifier or a keyword
> tile columns 3
3 models tiled
> surface
> transparency ~sel 75
> ~select
Nothing selected
> transparency 100
> transparency 0
> select #1:13,40,114 | #2:13,40,113 | #3:12,39,110
114 atoms, 111 bonds, 9 residues, 3 models selected
> color sel yellow
> ~select
Nothing selected
> coulombic
Coulombic values for 1ang_A SES surface #1.1: minimum, -8.04, mean 3.52,
maximum 19.83
Coulombic values for 7bfk_A SES surface #2.1: minimum, -23.67, mean 0.33,
maximum 14.40
Coulombic values for
rnaselike_DM_50091_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb_A SES
surface #3.1: minimum, -15.14, mean -0.74, maximum 10.53
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic
Coulombic values for 1ang_A SES surface #1.1: minimum, -8.04, mean 3.52,
maximum 19.83
Coulombic values for 7bfk_A SES surface #2.1: minimum, -23.67, mean 0.33,
maximum 14.40
Coulombic values for
rnaselike_DM_50091_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb_A SES
surface #3.1: minimum, -15.14, mean -0.74, maximum 10.53
To also show corresponding color key, enter the above coulombic command and
add key true
> ui windowfill toggle
> ~display #2:115-124
> ~surface #2:115-124
> ~ribbon #2:115-124
> surface
> delete #2:115-124
> coulombic
Coulombic values for 1ang_A SES surface #1.1: minimum, -8.04, mean 3.52,
maximum 19.83
Coulombic values for 7bfk_A SES surface #2.1: minimum, -23.08, mean 2.04,
maximum 15.03
Coulombic values for
rnaselike_DM_50091_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb_A SES
surface #3.1: minimum, -15.14, mean -0.74, maximum 10.53
To also show corresponding color key, enter the above coulombic command and
add key true
> select #1:13,40,114 | #2:13,40,113 | #3:12,39,110
114 atoms, 111 bonds, 9 residues, 3 models selected
> color sel yellow
> ~select
Nothing selected
> set bgColor white
> set bgColor #ffffff00
> lighting flat
> lighting shadows true intensity 0.5
> set bgColor white
> set bgColor gray
> set bgColor #80808000
> open
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/1ang_7bfk_dm_afold_mmaker_HKH.cxs
> set bgColor transparent
opened ChimeraX session
> ~ribbon ~sel
> ribbon
> transparency ~sel 75
> transparency ~sel 75 target c
> ~select
Nothing selected
> lighting flat
> set bgColor white
> set bgColor #ffffff00
> lighting flat
> lighting shadows true intensity 0.5
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> display
> ~ribbon
> show stick 0.3
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> ribbone
Unknown command: ribbone
> ribbon
> transparency 100
> transparency 100 target c
> transparency 0 target c
> mmaker #1 to #3 show 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
rnaselike_DM_50091_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain
A (#3) with 1ang, chain A (#1), sequence alignment score = 218.5
Alignment identifier is 3
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3
Hiding conservation header for alignment 3
Chains used in RMSD evaluation for alignment 3: 1ang #1/A,
rnaselike_DM_50091_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #3/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3
RMSD between 85 pruned atom pairs is 0.861 angstroms; (across all 108 pairs:
3.362)
Chains used in RMSD evaluation for alignment 1: 1ang #1/A, 7bfk #2/A
> color #2 byattr seq_rmsd
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> close all
> open 1ANG fromDatabase pdb
1ang title:
Crystal structure of human angiogenin reveals the structural basis for its
functional divergence from ribonuclease [more info...]
Chain information for 1ang #1
---
Chain | Description | UniProt
A | ANGIOGENIN | ANGI_HUMAN 1-123
1ang mmCIF Assemblies
---
1| author_defined_assembly
Associated 1ang chain A to 1ang, chain A with 0 mismatches
> open 7BFK fromDatabase pdb
7bfk title:
X-ray structure of SS-RNase-2 [more info...]
Chain information for 7bfk #2
---
Chain | Description | UniProt
A B | Angiogenin-1 | B5XAZ0_SALSA 1-126
7bfk mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
Associated 7bfk chain A to 7bfk, chain A with 0 mismatches
Associated 7bfk chain B to 7bfk, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 1: 1ang #1/A, 7bfk #2/A
Associated 7bfk chain A to 7bfk, chain A with 0 mismatches
Associated 7bfk chain B to 7bfk, chain A with 0 mismatches
> open 1AGI fromDatabase pdb
1agi title:
Crystal structure of bovine angiogenin At 1.5 angstroms resolution [more
info...]
Chain information for 1agi #3
---
Chain | Description | UniProt
A | ANGIOGENIN | ANG1_BOVIN 1-125
> open 4qfi fromDatabase pdb
4qfi title:
The crystal structure of rat angiogenin-heparin complex [more info...]
Chain information for 4qfi #4
---
Chain | Description | UniProt
A B | Angiogenin | Q5WRG2_RAT 0-121
Non-standard residues in 4qfi #4
---
ACY — acetic acid
ZN — zinc ion
4qfi mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> open 2bwk fromDatabase pdb
Summary of feedback from opening 2bwk fetched from pdb
---
warnings | Atom NH1 has no neighbors to form bonds with according to residue
template for ARG /A:88
Atom NH2 has no neighbors to form bonds with according to residue template for
ARG /A:88
note | Fetching compressed mmCIF 2bwk from
http://files.rcsb.org/download/2bwk.cif
2bwk title:
Murine angiogenin, sulphate complex [more info...]
Chain information for 2bwk #5
---
Chain | Description | UniProt
A | ANGIOGENIN | ANG1_MOUSE 1-121
Non-standard residues in 2bwk #5
---
SO4 — sulfate ion
> open 3zbv fromDatabase pdb
Summary of feedback from opening 3zbv fetched from pdb
---
note | Fetching compressed mmCIF 3zbv from
http://files.rcsb.org/download/3zbv.cif
3zbv title:
Crystal Structure of murine Angiogenin-2 [more info...]
Chain information for 3zbv #6
---
Chain | Description | UniProt
A | ANGIOGENIN-2 | ANG2_MOUSE 1-121
Non-standard residues in 3zbv #6
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
SO4 — sulfate ion
ZN — zinc ion
3zbv mmCIF Assemblies
---
1| author_and_software_defined_assembly
> open 2j4t fromDatabase pdb
Summary of feedback from opening 2j4t fetched from pdb
---
note | Fetching compressed mmCIF 2j4t from
http://files.rcsb.org/download/2j4t.cif
2j4t title:
Biological and Structural Features of Murine Angiogenin-4, an Angiogenic
Protein [more info...]
Chain information for 2j4t #7
---
Chain | Description | UniProt
A B | ANGIOGENIN-4 | Q80Z85_MOUSE -23-120
2j4t mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> open 3zbw fromDatabase pdb
Summary of feedback from opening 3zbw fetched from pdb
---
note | Fetching compressed mmCIF 3zbw from
http://files.rcsb.org/download/3zbw.cif
3zbw title:
Crystal Structure of murine Angiogenin-3 [more info...]
Chain information for 3zbw #8
---
Chain | Description | UniProt
A B | ANGIOGENIN-3 | ANG3_MOUSE 1-121
Non-standard residues in 3zbw #8
---
ACY — acetic acid
SO4 — sulfate ion
ZN — zinc ion
> open 4per fromDatabase pdb
4per title:
Structure of Gallus gallus ribonuclease inhibitor complexed with Gallus gallus
ribonuclease I [more info...]
Chain information for 4per #9
---
Chain | Description | UniProt
A | Ribonuclease Inhibitor | Q5ZIY8_CHICK 1-456
B | Angiogenin | ANGI_CHICK 3-115
> delete ~protein
> edl ~/a
Unknown command: edl ~/a
> delete ~/a
> close all
> open 1ANG fromDatabase pdb
1ang title:
Crystal structure of human angiogenin reveals the structural basis for its
functional divergence from ribonuclease [more info...]
Chain information for 1ang #1
---
Chain | Description | UniProt
A | ANGIOGENIN | ANGI_HUMAN 1-123
1ang mmCIF Assemblies
---
1| author_defined_assembly
Associated 1ang chain A to 1ang, chain A with 0 mismatches
> open 7BFK fromDatabase pdb
7bfk title:
X-ray structure of SS-RNase-2 [more info...]
Chain information for 7bfk #2
---
Chain | Description | UniProt
A B | Angiogenin-1 | B5XAZ0_SALSA 1-126
7bfk mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
Associated 7bfk chain A to 7bfk, chain A with 0 mismatches
Associated 7bfk chain B to 7bfk, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 1: 1ang #1/A, 7bfk #2/A
Associated 7bfk chain A to 7bfk, chain A with 0 mismatches
Associated 7bfk chain B to 7bfk, chain A with 0 mismatches
> open 1AGI fromDatabase pdb
1agi title:
Crystal structure of bovine angiogenin At 1.5 angstroms resolution [more
info...]
Chain information for 1agi #3
---
Chain | Description | UniProt
A | ANGIOGENIN | ANG1_BOVIN 1-125
> open 4qfi fromDatabase pdb
4qfi title:
The crystal structure of rat angiogenin-heparin complex [more info...]
Chain information for 4qfi #4
---
Chain | Description | UniProt
A B | Angiogenin | Q5WRG2_RAT 0-121
Non-standard residues in 4qfi #4
---
ACY — acetic acid
ZN — zinc ion
4qfi mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> open 2bwk fromDatabase pdb
Summary of feedback from opening 2bwk fetched from pdb
---
warnings | Atom NH1 has no neighbors to form bonds with according to residue
template for ARG /A:88
Atom NH2 has no neighbors to form bonds with according to residue template for
ARG /A:88
2bwk title:
Murine angiogenin, sulphate complex [more info...]
Chain information for 2bwk #5
---
Chain | Description | UniProt
A | ANGIOGENIN | ANG1_MOUSE 1-121
Non-standard residues in 2bwk #5
---
SO4 — sulfate ion
> open 3zbv fromDatabase pdb
3zbv title:
Crystal Structure of murine Angiogenin-2 [more info...]
Chain information for 3zbv #6
---
Chain | Description | UniProt
A | ANGIOGENIN-2 | ANG2_MOUSE 1-121
Non-standard residues in 3zbv #6
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
SO4 — sulfate ion
ZN — zinc ion
3zbv mmCIF Assemblies
---
1| author_and_software_defined_assembly
> open 2j4t fromDatabase pdb
2j4t title:
Biological and Structural Features of Murine Angiogenin-4, an Angiogenic
Protein [more info...]
Chain information for 2j4t #7
---
Chain | Description | UniProt
A B | ANGIOGENIN-4 | Q80Z85_MOUSE -23-120
2j4t mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> open 3zbw fromDatabase pdb
3zbw title:
Crystal Structure of murine Angiogenin-3 [more info...]
Chain information for 3zbw #8
---
Chain | Description | UniProt
A B | ANGIOGENIN-3 | ANG3_MOUSE 1-121
Non-standard residues in 3zbw #8
---
ACY — acetic acid
SO4 — sulfate ion
ZN — zinc ion
> open 4per fromDatabase pdb
4per title:
Structure of Gallus gallus ribonuclease inhibitor complexed with Gallus gallus
ribonuclease I [more info...]
Chain information for 4per #9
---
Chain | Description | UniProt
A | Ribonuclease Inhibitor | Q5ZIY8_CHICK 1-456
B | Angiogenin | ANGI_CHICK 3-115
> delete ~protein
> ~display
> hide all models
> show #1 models
> hide #1 models
> show #2 models
> delete #2:/b
Missing or invalid "atoms" argument: only initial part "#2" of atom specifier
valid
> delete #2/b
> show #3 models
> hide #2 models
> hide #3 models
> show #!4 models
> delete #4/b
> hide #!4 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #7 models
> delete #7/b
> hide #7 models
> show #7 models
> show #!8 models
> hide #7 models
> delete #8/b
> hide #!8 models
> show #!9 models
> delete #9/b
> close #9
> open 4per fromDatabase pdb
4per title:
Structure of Gallus gallus ribonuclease inhibitor complexed with Gallus gallus
ribonuclease I [more info...]
Chain information for 4per #9
---
Chain | Description | UniProt
A | Ribonuclease Inhibitor | Q5ZIY8_CHICK 1-456
B | Angiogenin | ANGI_CHICK 3-115
> delete #9/a
> mmaker #2-9 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 1ang, chain A (#1) with 7bfk, chain A (#2), sequence alignment
score = 236.6
RMSD between 86 pruned atom pairs is 0.827 angstroms; (across all 115 pairs:
3.945)
Matchmaker 1ang, chain A (#1) with 1agi, chain A (#3), sequence alignment
score = 481.4
RMSD between 116 pruned atom pairs is 0.482 angstroms; (across all 122 pairs:
1.854)
Matchmaker 1ang, chain A (#1) with 4qfi, chain A (#4), sequence alignment
score = 506.6
RMSD between 114 pruned atom pairs is 0.600 angstroms; (across all 116 pairs:
0.756)
Matchmaker 1ang, chain A (#1) with 2bwk, chain A (#5), sequence alignment
score = 527.3
RMSD between 114 pruned atom pairs is 0.637 angstroms; (across all 116 pairs:
0.775)
Matchmaker 1ang, chain A (#1) with 3zbv, chain A (#6), sequence alignment
score = 471.4
RMSD between 110 pruned atom pairs is 0.760 angstroms; (across all 118 pairs:
1.489)
Matchmaker 1ang, chain A (#1) with 2j4t, chain A (#7), sequence alignment
score = 476.9
RMSD between 109 pruned atom pairs is 0.614 angstroms; (across all 119 pairs:
1.038)
Matchmaker 1ang, chain A (#1) with 3zbw, chain A (#8), sequence alignment
score = 465.3
RMSD between 115 pruned atom pairs is 0.708 angstroms; (across all 120 pairs:
1.928)
Matchmaker 1ang, chain A (#1) with 4per, chain B (#9), sequence alignment
score = 231.6
RMSD between 85 pruned atom pairs is 0.934 angstroms; (across all 103 pairs:
3.344)
> ribbon
> show all models
> open
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/1ang_7bfk_dm_afold_mmaker_HKH.cxs
> set bgColor transparent
opened ChimeraX session
> hide #2 models
> coulombic sel & #1,3
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 1ang_A SES surface #1.1: minimum, -8.04, mean 3.52,
maximum 19.83
Coulombic values for
rnaselike_DM_50091_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb_A SES
surface #3.1: minimum, -15.14, mean -0.74, maximum 10.53
To also show corresponding color key, enter the above coulombic command and
add key true
> surface
> tile
2 models tiled
Chains used in RMSD evaluation for alignment 2: 7bfk #2/A,
rnaselike_DM_50091_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #3/A
Chains used in RMSD evaluation for alignment 1: 1ang #1/A, 7bfk #2/A
> close all
> open
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/1dza.cif
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/1gv7.cif
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/1h53.cif
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/2bwl.cif
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/2j4t.cif
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/2k11.cif
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/2q4g.cif
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/2zpo.cif
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/3lje.cif
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/3ln8.cif
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/3tsr.cif
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/3zbv.cif
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/3zbw.cif
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/4kxh.cif
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/4qfi.cif
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/4qfj.cif
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/5m9m.cif
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/5m9s.cif
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/7bfk.cif
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/pdb70_a3m.ffdata
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/pdb70_a3m.ffindex
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/pdb70_cs219.ffdata
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/pdb70_cs219.ffindex
Unrecognized file suffix '.ffdata'
> open
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/1dza.cif
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/1gv7.cif
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/1h53.cif
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/2bwl.cif
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/2j4t.cif
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/2k11.cif
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/2q4g.cif
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/2zpo.cif
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/3lje.cif
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/3ln8.cif
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/3tsr.cif
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/3zbv.cif
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/3zbw.cif
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/4kxh.cif
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/4qfi.cif
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/4qfj.cif
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/5m9m.cif
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/5m9s.cif
> /home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/7bfk.cif
Summary of feedback from opening
/home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/1gv7.cif
---
notes | Fetching CCD PCA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/PCA/PCA.cif
Fetching CCD CIT from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/T/CIT/CIT.cif
Summary of feedback from opening
/home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/4qfj.cif
---
notes | Fetching CCD SGN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/SGN/SGN.cif
Fetching CCD IDS from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/IDS/IDS.cif
Summary of feedback from opening
/home/arfalas/ang_work/struct/rnasedlike_DM/rnaselike_DM_50091/rnaselike_DM_50091_all/templates_101/5m9m.cif
---
notes | Fetching CCD PGE from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/PGE/PGE.cif
Fetching CCD BTB from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/B/BTB/BTB.cif
1dza.cif title:
3-D structure of a HP-RNase [more info...]
Chain information for 1dza.cif #1
---
Chain | Description | UniProt
A B | RIBONUCLEASE 1 | RNAS1_HUMAN 100-228
1dza.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
1gv7.cif title:
ARH-I, an angiogenin/RNase A chimera [more info...]
Chain information for 1gv7.cif #2
---
Chain | Description | UniProt
A | ANGIOGENIN | ANGI_HUMAN 1-57 71-123, RNP_BOVIN 58-70
Non-standard residues in 1gv7.cif #2
---
CIT — citric acid
1h53.cif title:
Binding of Phosphate and Pyrophosphate ions at the active site of human
Angiogenin as revealed by X-ray Crystallography [more info...]
Chain information for 1h53.cif #3
---
Chain | Description | UniProt
A | ANGIOGENIN | ANGI_HUMAN 2-123
Non-standard residues in 1h53.cif #3
---
CIT — citric acid
PO4 — phosphate ion
2bwl.cif title:
Murine angiogenin, phosphate complex [more info...]
Chain information for 2bwl.cif #4
---
Chain | Description | UniProt
A | ANGIOGENIN | ANG1_MOUSE 1-121
Non-standard residues in 2bwl.cif #4
---
PO4 — phosphate ion
2j4t.cif title:
Biological and Structural Features of Murine Angiogenin-4, an Angiogenic
Protein [more info...]
Chain information for 2j4t.cif #5
---
Chain | Description | UniProt
A B | ANGIOGENIN-4 | Q80Z85_MOUSE -23-120
2j4t.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
2k11.cif title:
Solution structure of human pancreatic ribonuclease [more info...]
Chain information for 2k11.cif
---
Chain | Description | UniProt
6.1/A 6.2/A 6.3/A 6.4/A 6.5/A 6.6/A 6.7/A 6.8/A 6.9/A 6.10/A 6.11/A 6.12/A
6.13/A 6.14/A 6.15/A 6.16/A 6.17/A 6.18/A 6.19/A 6.20/A | Pancreatic
Ribonuclease | RNAS1_HUMAN 1-127
2q4g.cif title:
Ensemble refinement of the protein crystal structure of human ribonuclease
inhibitor complexed with ribonuclease I [more info...]
Chain information for 2q4g.cif
---
Chain | Description | UniProt
7.1/W 7.2/W 7.3/W 7.4/W 7.5/W 7.6/W 7.7/W 7.8/W 7.1/Y 7.2/Y 7.3/Y 7.4/Y 7.5/Y
7.6/Y 7.7/Y 7.8/Y | Ribonuclease inhibitor | RINI_HUMAN 0-460
7.1/X 7.2/X 7.3/X 7.4/X 7.5/X 7.6/X 7.7/X 7.8/X 7.1/Z 7.2/Z 7.3/Z 7.4/Z 7.5/Z
7.6/Z 7.7/Z 7.8/Z | Ribonuclease pancreatic | RNAS1_HUMAN 1-128
2zpo.cif title:
Crystal Structure of Green Turtle Egg White Ribonuclease [more info...]
Chain information for 2zpo.cif #8
---
Chain | Description | UniProt
A | Ribonuclease | RNAS1_CHEMY 1-119
Non-standard residues in 2zpo.cif #8
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
SO4 — sulfate ion
2zpo.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| software_defined_assembly
3lje.cif title:
The X-ray structure of zebrafish RNase5 [more info...]
Chain information for 3lje.cif #9
---
Chain | Description
A | Zebrafish RNase5
Non-standard residues in 3lje.cif #9
---
ACT — acetate ion
SO4 — sulfate ion
3ln8.cif title:
The X-ray structure of Zf-RNase-1 from a new crystal form at pH 7.3 [more
info...]
Chain information for 3ln8.cif #10
---
Chain | Description
A B | HYDROLASE
Non-standard residues in 3ln8.cif #10
---
SO4 — sulfate ion
3ln8.cif mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| software_defined_assembly
3tsr.cif title:
X-ray structure of mouse ribonuclease inhibitor complexed with mouse
ribonuclease 1 [more info...]
Chain information for 3tsr.cif #11
---
Chain | Description | UniProt
A B C D | Ribonuclease pancreatic | RNAS1_MOUSE 2-125
E F G H | Ribonuclease inhibitor | RINI_MOUSE 1-456
Non-standard residues in 3tsr.cif #11
---
EDO — 1,2-ethanediol (ethylene glycol)
PEG — di(hydroxyethyl)ether
3tsr.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
4| author_defined_assembly
3zbv.cif title:
Crystal Structure of murine Angiogenin-2 [more info...]
Chain information for 3zbv.cif #12
---
Chain | Description | UniProt
A | ANGIOGENIN-2 | ANG2_MOUSE 1-121
Non-standard residues in 3zbv.cif #12
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
SO4 — sulfate ion
ZN — zinc ion
3zbv.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
3zbw.cif title:
Crystal Structure of murine Angiogenin-3 [more info...]
Chain information for 3zbw.cif #13
---
Chain | Description | UniProt
A B | ANGIOGENIN-3 | ANG3_MOUSE 1-121
Non-standard residues in 3zbw.cif #13
---
ACY — acetic acid
SO4 — sulfate ion
ZN — zinc ion
4kxh.cif title:
The X-ray crystal structure of a dimeric variant of human pancreatic
ribonuclease [more info...]
Chain information for 4kxh.cif #14
---
Chain | Description | UniProt
A B C D | Ribonuclease pancreatic | RNAS1_HUMAN 1-128
Non-standard residues in 4kxh.cif #14
---
CL — chloride ion
NA — sodium ion
SO4 — sulfate ion
4kxh.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
4qfi.cif title:
The crystal structure of rat angiogenin-heparin complex [more info...]
Chain information for 4qfi.cif #15
---
Chain | Description | UniProt
A B | Angiogenin | Q5WRG2_RAT 0-121
Non-standard residues in 4qfi.cif #15
---
ACY — acetic acid
ZN — zinc ion
4qfi.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
4qfj.cif title:
The crystal structure of rat angiogenin-heparin complex [more info...]
Chain information for 4qfj.cif #16
---
Chain | Description | UniProt
A B | Angiogenin | Q5WRG2_RAT 0-121
Non-standard residues in 4qfj.cif #16
---
ACY — acetic acid
IDS — 2-O-sulfo-alpha-L-idopyranuronic acid (O2-SULFO-GLUCURONIC ACID;
2-O-sulfo-alpha-L-iduronic acid; 2-O-sulfo-L-iduronic acid; 2-O-sulfo-iduronic
acid)
SGN — 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose (N,O6-DISULFO-
GLUCOSAMINE; 6-O-sulfo-N-sulfo-alpha-D-glucosamine;
2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucose;
2-deoxy-6-O-sulfo-2-(sulfoamino)-D-glucose;
2-deoxy-6-O-sulfo-2-(sulfoamino)-glucose)
ZN — zinc ion
5m9m.cif title:
Human angiogenin PD variant Q77P [more info...]
Chain information for 5m9m.cif #17
---
Chain | Description | UniProt
A B C D | Angiogenin | ANGI_HUMAN 1-123
Non-standard residues in 5m9m.cif #17
---
BTB — 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol (bis-
tris buffer)
EDO — 1,2-ethanediol (ethylene glycol)
PGE — triethylene glycol
SO4 — sulfate ion
5m9m.cif mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
4| author_defined_assembly
5m9s.cif title:
Human angiogenin ALS variant V103I [more info...]
Chain information for 5m9s.cif #18
---
Chain | Description | UniProt
A | Angiogenin | ANGI_HUMAN 1-123
Non-standard residues in 5m9s.cif #18
---
TAR — D(-)-tartaric acid
7bfk.cif title:
X-ray structure of SS-RNase-2 [more info...]
Chain information for 7bfk.cif #19
---
Chain | Description | UniProt
A B | Angiogenin-1 | B5XAZ0_SALSA 1-126
7bfk.cif mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
Associated 1h53.cif chain A to 1ang, chain A with 1 mismatch
Associated 5m9m.cif chain A to 1ang, chain A with 1 mismatch
Associated 5m9m.cif chain B to 1ang, chain A with 1 mismatch
Associated 5m9m.cif chain C to 1ang, chain A with 1 mismatch
Associated 5m9m.cif chain D to 1ang, chain A with 1 mismatch
Associated 5m9s.cif chain A to 1ang, chain A with 1 mismatch
Associated 7bfk.cif chain A to 7bfk, chain A with 0 mismatches
Associated 7bfk.cif chain B to 7bfk, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 1: 1h53.cif #3/A, 5m9m.cif #17/A,
5m9s.cif #18/A, 7bfk.cif #19/B
Associated 7bfk.cif chain A to 7bfk, chain A with 0 mismatches
Associated 7bfk.cif chain B to 7bfk, chain A with 0 mismatches
> hide all
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===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.7.dev202307110732 (2023-07-11)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.2 (Core Profile) Mesa 23.1.6-1
OpenGL renderer: Mesa Intel(R) HD Graphics 4000 (IVB GT2)
OpenGL vendor: Intel
Python: 3.11.2
Locale: it_IT.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb
XDG_SESSION_TYPE=tty
DESKTOP_SESSION=
XDG_SESSION_DESKTOP=
XDG_CURRENT_DESKTOP=
DISPLAY=:0
Manufacturer: LENOVO
Model: 232566G
OS: Debian GNU/Linux n/a trixie
Architecture: 64bit ELF
Virtual Machine: none
CPU: 4 Intel(R) Core(TM) i7-3520M CPU @ 2.90GHz
Cache Size: 4096 KB
Memory:
total used free shared buff/cache available
Mem: 15Gi 6.0Gi 3.4Gi 238Mi 6.6Gi 9.4Gi
Swap: 7.4Gi 0B 7.4Gi
Graphics:
00:02.0 VGA compatible controller [0300]: Intel Corporation 3rd Gen Core processor Graphics Controller [8086:0166] (rev 09)
Subsystem: Lenovo 3rd Gen Core processor Graphics Controller [17aa:21fa]
Kernel driver in use: i915
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2023.5.7
cftime: 1.6.2
charset-normalizer: 3.2.0
ChimeraX-AddCharge: 1.5.11
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.46
ChimeraX-AtomicLibrary: 10.0.7
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.3
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.dev202307110732
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.2
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.7
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.2
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.9
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.30.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.1.0
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
distro: 1.7.0
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.40.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.9.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2023.3.16
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.7
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.3.1
jupyterlab-widgets: 3.0.8
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 23.1
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.8.1
prompt-toolkit: 3.0.39
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.6
PyOpenGL-accelerate: 3.1.6
pyparsing: 3.1.0
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.1.0
qtconsole: 5.4.3
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.9.3
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.2
traitlets: 5.9.0
typing-extensions: 4.7.1
tzdata: 2023.3
urllib3: 2.0.3
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.8
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash processing atomic changes data |
comment:2 by , 2 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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Hi Bruno,
--Eric