![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 74 minutes ago
#20830 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-26.5.1-arm64-arm-64bit
ChimeraX Version: 1.12 (2026-06-12 03:42:34 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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"name" : "libXau.6.dylib"
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{
"source" : "P",
"arch" : "arm64e",
"base" : 6485544960,
"size" : 250544,
"uuid" : "cc1cf985-bc65-3725-809f-4c1e36b8f4ba",
"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6485798912,
"size" : 52028,
"uuid" : "4f33683c-18c8-39a1-800b-2e3bd43bcc13",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
},
{
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"arch" : "arm64e",
"base" : 6484312064,
"size" : 527776,
"uuid" : "694b7881-1bf3-3d0f-8f19-b50ae4e8ef8a",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
},
{
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"arch" : "arm64e",
"base" : 6481772544,
"size" : 680472,
"uuid" : "a237ef81-b68b-37ba-a165-92c965529534",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
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"source" : "A",
"base" : 0,
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],
"sharedCache" : {
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"size" : 5990596608,
"uuid" : "ff7119a7-f64d-305d-8135-7e6eb1c207d1"
},
"legacyInfo" : {
"threadTriggered" : {
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "e8717755549d2b003f7e9553f50423b49e76b713",
"bug_type" : "309",
"roots_installed" : 0,
"trmStatus" : 1,
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "642da32dea3b2418c750f848",
"factorPackIds" : [
"66d8b2f77cd4b62688efd2cf"
],
"deploymentId" : 240000011
},
{
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"factorPackIds" : [
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],
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}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.12 (2026-06-12)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/hwu/Desktop/HeightDB/result-0nvi6/3GJF and 0nvi6.cxs" format
> session
> view name session-start
opened ChimeraX session
> hide #1 models
> show #1 models
> hide #!2 models
> show #!2 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> open
> /Users/hwu/Downloads/test_77ace/test_77ace_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
> format pdb
No such file/path:
/Users/hwu/Downloads/test_77ace/test_77ace_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
> open "/Users/hwu/Desktop/HeightDB/result-0nvi6/3GJF and 0nvi6.cxs" format
> session
> view name session-start
opened ChimeraX session
> open
> /Users/hwu/Desktop/HeightDB/test_77ace/test_77ace_scores_rank_001_alphafold2_ptm_model_2_seed_000.json
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open
/Users/hwu/Desktop/HeightDB/test_77ace/test_77ace_scores_rank_001_alphafold2_ptm_model_2_seed_000.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> open
> /Users/hwu/Desktop/HeightDB/test_77ace/test_77ace_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
Chain information for
test_77ace_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb #3
---
Chain | Description
A | No description available
Computing secondary structure
> matchmaker #3 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 3gjf, chain M (#2) with
test_77ace_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb, chain A (#3),
sequence alignment score = 622.8
RMSD between 102 pruned atom pairs is 0.290 angstroms; (across all 218 pairs:
25.827)
> hide #1 models
> hide #3 models
> show #3 models
> 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 #3 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #3 models
> select #2/D:245
5 atoms, 4 bonds, 1 residue, 1 model selected
> open /Users/hwu/Downloads/linker.fasta
Failed opening file /Users/hwu/Downloads/linker.fasta:
Sequence 'DP03824' differs in length from preceding sequences, and it is
therefore impossible to open these sequences as an alignment. If you want to
open the sequences individually, specify 'false' as the value of the
'alignment' keyword in the 'open' command.
> open /Users/hwu/Downloads/linker.fasta
Failed opening file /Users/hwu/Downloads/linker.fasta:
Sequence 'DP03824' differs in length from preceding sequences, and it is
therefore impossible to open these sequences as an alignment. If you want to
open the sequences individually, specify 'false' as the value of the
'alignment' keyword in the 'open' command.
> close session
> open 1yjd
Summary of feedback from opening 1yjd fetched from pdb
---
note | Fetching compressed mmCIF 1yjd from http://files.rcsb.org/download/1yjd.cif
1yjd title:
Crystal structure of human CD28 in complex with the Fab fragment of a
mitogenic antibody (5.11A1) [more info...]
Chain information for 1yjd #1
---
Chain | Description | UniProt
C | T-cell-specific surface glycoprotein CD28 | CD28_HUMAN -1-134
H | Fab fragment of 5.11A1 antibody heavy chain |
L | Fab fragment of 5.11A1 antibody light chain |
Non-standard residues in 1yjd #1
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
1yjd mmCIF Assemblies
---
1| author_defined_assembly
> select /C
1029 atoms, 1017 bonds, 159 residues, 1 model selected
> select clear
> select /C:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /C:118
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /C
Alignment identifier is 1/C
> select /C:14
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /C:14
12 atoms, 12 bonds, 1 residue, 1 model selected
> color bfactor sel
12 atoms, 1 residues, atom bfactor range 48.7 to 64.7
> select clear
> color bfactor
4493 atoms, 753 residues, atom bfactor range 25.8 to 100
> delete #1/A,B
> delete #1/A
> delete /A
> select /L:110
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete #1/H
> delete #1/L
> sequence chain #1/C
Destroying pre-existing alignment with identifier 1/C
Alignment identifier is 1/C
> sequence chain #1/C
Destroying pre-existing alignment with identifier 1/C
Alignment identifier is 1/C
> setattr /C uniprot
Missing or invalid "attrName" argument: Expected a text string
> setattr /C
Missing or invalid "target" argument: Expected a text string
> setattr #1/C uniprot
Missing or invalid "attrName" argument: Expected a text string
> setattr uniprot
Missing or invalid "attrName" argument: Expected a text string
> resnumbering
Unknown command: resnumbering
> setattr 1/C resnumbeirng
Missing or invalid "attrValue" argument: Expected a text string
> setattr 1/C resnumbering
Missing or invalid "attrValue" argument: Expected a text string
> setattr 1/C resnumbering=uniprot
Missing or invalid "attrValue" argument: Expected a text string
> open P10747 fromDatabase uniprot
Summary of feedback from opening P10747 fetched from uniprot
---
notes | Fetching compressed P10747 UniProt info from https://www.uniprot.org/uniprot/P10747.xml
Alignment identifier is P10747
Associated 1yjd chain C to P10747 with 4 mismatches
Opened UniProt P10747
> select /C:22,48,68,94
24 atoms, 22 bonds, 4 residues, 1 model selected
> select /C:1-118
949 atoms, 972 bonds, 118 residues, 1 model selected
> select /C:22,48,68,94
24 atoms, 22 bonds, 4 residues, 1 model selected
> select /C:86-88
24 atoms, 23 bonds, 3 residues, 1 model selected
> ~select
Nothing selected
> select /C:19,53,74,87,111
40 atoms, 35 bonds, 5 residues, 1 model selected
> select /C:22,48,68,94
24 atoms, 22 bonds, 4 residues, 1 model selected
> select /C:106
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /C:106-112
52 atoms, 51 bonds, 7 residues, 1 model selected
> select clear
> select /C:102
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /C:102-118
135 atoms, 138 bonds, 17 residues, 1 model selected
> close session
> open "/Users/hwu/Desktop/HeightDB/result-0nvi6/3GJF and 0nvi6.cxs" format
> session
No such file/path: /Users/hwu/Desktop/HeightDB/result-0nvi6/3GJF and 0nvi6.cxs
> open
> /Users/hwu/Desktop/HeightDB/test_77ace/test_77ace_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
> format pdb
No such file/path:
/Users/hwu/Desktop/HeightDB/test_77ace/test_77ace_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
> open "/Users/hwu/Desktop/Structure prediction for
> HeightDB/Boltz2/result-0nvi6/3GJF and 0nvi6.cxs"
> view name session-start
opened ChimeraX session
> hide #!2 models
> show #!2 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> open "/Users/hwu/Desktop/Structure prediction for
> HeightDB/AF2/test_d6f2a/test_d6f2a_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"
Chain information for
test_d6f2a_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb #3
---
Chain | Description
A | No description available
Computing secondary structure
> matchmaker #3 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 3gjf, chain M (#2) with
test_d6f2a_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb, chain A (#3),
sequence alignment score = 631.1
RMSD between 101 pruned atom pairs is 0.315 angstroms; (across all 218 pairs:
26.487)
> hide #3 models
> show #3 models
> hide #3 models
> hide #!2 models
> show #3 models
> show #!2 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #3 models
> color bfactor #3
4550 atoms, 307 residues, atom bfactor range 30.4 to 98.6
> select #3/A:251
22 atoms, 21 bonds, 1 residue, 1 model selected
> sequence chain #3/A
Alignment identifier is 3/A
> select #3/A:58
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:58-59
18 atoms, 17 bonds, 2 residues, 1 model selected
> select
> #3/A:5-9,12-14,20-27,35-41,47-53,60-62,70-75,80-85,94-101,115-119,147-150,156-161,173-178,185-188,202-207,210-215,224-232,235-238,242-246,268-270,288-290
1790 atoms, 1791 bonds, 114 residues, 1 model selected
> select clear
> select #3/A:251
22 atoms, 21 bonds, 1 residue, 1 model selected
> info residues sel attribute bfactor
> info residues sel attribute bfactor
> ui tool show "Render/Select by Attribute"
> select #3/A:199
14 atoms, 14 bonds, 1 residue, 1 model selected
Populating font family aliases took 175 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.
> select clear
> select #3/A:248
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select #3/A:233
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:269
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #3/A:270
15 atoms, 14 bonds, 1 residue, 1 model selected
> select clear
> select #3/A:248
7 atoms, 6 bonds, 1 residue, 1 model selected
> close session
> open "/Users/hwu/Desktop/Structure prediction for
> HeightDB/Boltz2/result-0nvi6/3GJF and 0nvi6.cxs" format session
No such file/path: /Users/hwu/Desktop/Structure prediction for
HeightDB/Boltz2/result-0nvi6/3GJF and 0nvi6.cxs
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/3GJF and 0nvi6.cxs"
> view name session-start
opened ChimeraX session
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/AF2/test_d6f2a/test_d6f2a_pae.png"
Image mode RGBA is not supported (L, P, I;16, I;16B, I;16L, I;16S, F, F;32BF,
I, RGB)
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/AF2/test_d6f2a/test_d6f2a_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"
Chain information for
test_d6f2a_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb #3
---
Chain | Description
A | No description available
Computing secondary structure
> matchmaker #3 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 3gjf, chain M (#2) with
test_d6f2a_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb, chain A (#3),
sequence alignment score = 631.1
RMSD between 101 pruned atom pairs is 0.315 angstroms; (across all 218 pairs:
26.487)
> hide #1 models
> hide #3 models
> show #3 models
> hide #!2 models
> show #!2 models
> hide #3 models
> show #3 models
> save "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/3GJF 0nvi6 d6f2a.cxs"
> hide #!2 models
> color bfactor #3
4550 atoms, 307 residues, atom bfactor range 30.4 to 98.6
> ui tool show Distances
Exactly two atoms must be selected!
> select #3/A:181
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:263
12 atoms, 11 bonds, 1 residue, 1 model selected
> select add #3/A:180
26 atoms, 25 bonds, 2 residues, 1 model selected
> select add #3/A:181
33 atoms, 31 bonds, 3 residues, 1 model selected
> select subtract #3/A:180
19 atoms, 17 bonds, 2 residues, 1 model selected
Exactly two atoms must be selected!
> select clear
> select #3/A:181
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/A:181
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:181 @Ca
1 atom, 1 residue, 1 model selected
> select add #3/A:262
13 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> select #3/A:181 @Ca #3/A:262 @Ca
2 atoms, 2 residues, 1 model selected
> distance #3/A:181@CA #3/A:262@CA
Distance between
test_d6f2a_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb #3/A GLY 181
CA and ASP 262 CA: 31.177Å
> ~distance #3/A:181@CA #3/A:262@CA
> sequence chain #3/A
Alignment identifier is 3/A
> show #!2 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> copy #2
Unknown command: copy #2
> combine #2
> hide #!2 models
> hide #3 models
> select #4/M:48
7 atoms, 6 bonds, 1 residue, 1 model selected
> delete #4/M
> select #4/K:107
7 atoms, 6 bonds, 1 residue, 1 model selected
> delete #4/K
> show #3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #3 models
> hide #!2 models
> show #!4 models
> show #!2 models
> hide #!2 models
> show #3 models
> combine #23
No structures specified
> combine #3
> combine #4 #5
> hide #5 models
> hide #!4 models
> hide #3 models
> save "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/3GJF 0nvi6 d6f2a.cxs"
> show #1 models
> show #!2 models
> hide #!2 models
> hide #1 models
> show #1 models
> show #!2 models
> show #3 models
> hide #3 models
> hide #!6 models
> hide #!2 models
> hide #1 models
> select add #1
5078 atoms, 5211 bonds, 640 residues, 1 model selected
> select add #2
12262 atoms, 11770 bonds, 2257 residues, 2 models selected
> select add #3
16812 atoms, 16378 bonds, 2564 residues, 3 models selected
> select add #4
20378 atoms, 19635 bonds, 3351 residues, 4 models selected
> select add #5
24928 atoms, 24243 bonds, 3658 residues, 5 models selected
> select subtract #5
20378 atoms, 19635 bonds, 3351 residues, 4 models selected
> select add #5
24928 atoms, 24243 bonds, 3658 residues, 5 models selected
> close #5
> close #1
> close #2
> close #3
> close #4
> show #!6 models
> select add #6
8116 atoms, 7865 bonds, 1094 residues, 1 model selected
> select clear
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/Sequences/rcsb_pdb_3GJF.fasta"
Failed opening file /Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group
Folder/Data for Young-wook/Harry Wu/Collaborations/Structure prediction for
HeightDB/Sequences/rcsb_pdb_3GJF.fasta:
Sequence '3GJF_4|Chains G[auth K], H[auth L]|Antibody light chain|Homo sapiens
(9606)' differs in length from preceding sequences, and it is therefore
impossible to open these sequences as an alignment. If you want to open the
sequences individually, specify 'false' as the value of the 'alignment'
keyword in the 'open' command.
> sequence chain #6/D
Alignment identifier is 6/D
> sequence chain #6/E
Alignment identifier is 6/E
> sequence chain #6/F
Alignment identifier is 6/F
> sequence chain #6/A
Alignment identifier is 6/A
> select /A:248
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:248-307
919 atoms, 935 bonds, 60 residues, 1 model selected
> delete #6/A:248-307
> sequence chain #6/D
Alignment identifier is 6/D
> sequence chain #6/E
Alignment identifier is 6/E
> sequence chain #6/F
Alignment identifier is 6/F
> sequence chain #6/A
Destroying pre-existing alignment with identifier 6/A
Alignment identifier is 6/A
> select /D:251
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /D:251-276
217 atoms, 224 bonds, 26 residues, 1 model selected
> select /D:1
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /D:1-60
495 atoms, 512 bonds, 60 residues, 1 model selected
> select clear
> color bfactor
7197 atoms, 1034 residues, atom bfactor range 14.8 to 98.6
> save "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/3GJF d6f2a.cxs"
> save "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/3GJF d6f2a.cif" relModel #6
Not saving entity_poly_seq for non-authoritative sequences
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/3GJF_d6f2a_measure.cxc"
> open 3GJF_d6f2a.cif
Failed opening file /Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group
Folder/Data for Young-wook/Harry Wu/Collaborations/Structure prediction for
HeightDB/ChimeraX/3GJF_d6f2a_measure.cxc:
No such file/path: 3GJF_d6f2a.cif
> close session
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/3GJF_d6f2a_measure.cxc"
> open 3GJF_d6f2a.cif
No such file/path: 3GJF_d6f2a.cif
> open /Users/hwu/Desktop/measure_ecd.py
Traceback (most recent call last):
File "/Users/hwu/Desktop/measure_ecd.py", line 26, in
from Bio.PDB import PDBParser, MMCIFParser
ModuleNotFoundError: No module named 'Bio'
Failed opening file /Users/hwu/Desktop/measure_ecd.py:
Error opening python file /Users/hwu/Desktop/measure_ecd.py
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/3GJF_d6f2a_measure.cxc"
> open 3GJF_d6f2a.cif
Summary of feedback from opening 3GJF_d6f2a.cif
---
warnings | Unknown polymer entity '4' on line 4488
Missing or incorrect sequence information. Inferred polymer connectivity.
Atom H is not in the residue template for MET /A:1
Chain information for 3GJF_d6f2a.cif #1
---
Chain | Description
A | No description available
D | HLA class I histocompatibility antigen, A-2 alpha chain
E | Beta-2-microglobulin
F | NYESO-1 peptide
> color #1 bychain
> color ~#1:0-276 #808080 transparency 70 target ac
> shape cylinder radius 1.0 fromPoint 38.94,2.55,29.79 toPoint
> -52.11,43.45,48.41 color yellow
> shape sphere radius 2.5 center 38.94,2.55,29.79 color red
> shape sphere radius 2.5 center -52.11,43.45,48.41 color red
> 2dlabels text "3GJF_d6f2a: 10.15 nm" xpos 0.05 ypos 0.9 color black size 24
> view
executed 3GJF_d6f2a_measure.cxc
> ui tool show Distances
> close session
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/3GJF d6f2a.cif" format mmcif
No such file/path: /Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group
Folder/Data for Young-wook/Harry Wu/Collaborations/Structure prediction for
HeightDB/ChimeraX/3GJF d6f2a.cif
> open 3gjf
3gjf title:
Rational development of high-affinity T-cell receptor-like antibodies [more
info...]
Chain information for 3gjf #1
---
Chain | Description | UniProt
A D | HLA class I histocompatibility antigen, A-2 alpha chain | 1A02_HUMAN 1-276
B E | Beta-2-microglobulin | B2MG_HUMAN 1-99
C F | NYESO-1 peptide |
H M | Antibody heavy chain |
K L | Antibody light chain |
3gjf mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> hide surfaces
> select ::name="HOH"
1603 atoms, 1603 residues, 1 model selected
> select /D:1380@O
1 atom, 1 residue, 1 model selected
> select ::name="HOH"
1603 atoms, 1603 residues, 1 model selected
> hide sel
> hide sel atoms
> select clear
> hide cartoons
> show cartoons
> hide surfaces
> hide atoms
> select clear
> select /H:164
5 atoms, 4 bonds, 1 residue, 1 model selected
> delete #1/H
> select /L:73
5 atoms, 4 bonds, 1 residue, 1 model selected
> delete #1/L
> select /A:116
12 atoms, 12 bonds, 1 residue, 1 model selected
> delete #1/A
> select clear
> select /C:3
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete #1/C
> select /B:55
6 atoms, 5 bonds, 1 residue, 1 model selected
> delete #1/B
> select /M:48
7 atoms, 6 bonds, 1 residue, 1 model selected
> delete #1/M
> select /K:76
7 atoms, 6 bonds, 1 residue, 1 model selected
> delete #1/K
> save "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/3GJF_HLA A*2:01_only.cif" relModel #1
> close session
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/3GJF_HLA_A*201_only_measure.cxc"
> open 3GJF_HLA_A*201_only.cif
Chain information for 3GJF_HLA_A*201_only.cif #1
---
Chain | Description
D | HLA class I histocompatibility antigen, A-2 alpha chain
E | Beta-2-microglobulin
F | NYESO-1 peptide
3GJF_HLA_A*201_only.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> color #1 bychain
> color ~#1:0-276 #808080 transparency 70 target ac
> shape cylinder radius 1.0 fromPoint 39.24,8.14,34.22 toPoint
> -26.71,25.38,37.76 color yellow
> shape sphere radius 2.5 center 39.24,8.14,34.22 color red
> shape sphere radius 2.5 center -26.71,25.38,37.76 color red
> 2dlabels text "3GJF_HLA_A*201_only: 6.83 nm" xpos 0.05 ypos 0.9 color black
> size 24
> view
executed 3GJF_HLA_A*201_only_measure.cxc
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/CD2CD58merge_measure.cxc"
> open CD2CD58merge.cif
Summary of feedback from opening CD2CD58merge.cif
---
warnings | Unknown polymer entity '1' on line 112
Unknown polymer entity '2' on line 1374
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for CD2CD58merge.cif #6
---
Chain | Description
A | HUMAN CD2 PROTEIN
B | HUMAN CD58 PROTEIN
> color #1 bychain
> color ~#1:1-215 #808080 transparency 70 target ac
> shape cylinder radius 1.0 fromPoint 6.92,-7.59,89.20 toPoint
> 68.86,44.41,-34.22 color yellow
> shape sphere radius 2.5 center 6.92,-7.59,89.20 color red
> shape sphere radius 2.5 center 68.86,44.41,-34.22 color red
> 2dlabels text "CD2CD58merge: 14.76 nm" xpos 0.05 ypos 0.9 color black size
> 24
> view
executed CD2CD58merge_measure.cxc
> select add #1
3566 atoms, 3257 bonds, 787 residues, 1 model selected
> select add #2
3566 atoms, 3257 bonds, 787 residues, 2 models selected
> select add #3
3566 atoms, 3257 bonds, 787 residues, 3 models selected
> select add #4
3566 atoms, 3257 bonds, 787 residues, 4 models selected
> select add #5
3566 atoms, 3257 bonds, 787 residues, 7 models selected
> select clear
> hide #1 models
> hide #2 models
> hide #4 models
> hide #3 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> close session
> open /Users/hwu/Desktop/HeightDB/CD2CD58merge_measure.cxc format cmd
No such file/path: /Users/hwu/Desktop/HeightDB/CD2CD58merge_measure.cxc
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/CD2CD58merge_measure.cxc"
> open CD2CD58merge.cif
Summary of feedback from opening CD2CD58merge.cif
---
warnings | Unknown polymer entity '1' on line 112
Unknown polymer entity '2' on line 1374
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for CD2CD58merge.cif #1
---
Chain | Description
A | HUMAN CD2 PROTEIN
B | HUMAN CD58 PROTEIN
> color #1 bychain
> color ~#1:1-215 #808080 transparency 70 target ac
> shape cylinder radius 1.0 fromPoint 6.92,-7.59,89.20 toPoint
> 68.86,44.41,-34.22 color yellow
> shape sphere radius 2.5 center 6.92,-7.59,89.20 color red
> shape sphere radius 2.5 center 68.86,44.41,-34.22 color red
> 2dlabels text "CD2CD58merge: 14.76 nm" xpos 0.05 ypos 0.9 color black size
> 24
> view
executed CD2CD58merge_measure.cxc
> close session
> alphafold fetch AF-Q9Y287-F1
Unrecognized format for AlphaFold id "AF-Q9Y287-F1". Example AlphaFold ids
P29474, Q8N9C0-2, IGS22_HUMAN, AF-Q8N9C0-F1-v6, AF-Q8N9C0-2-F1-v6.
> alphafold fetch AF-Q9Y287-F1-v6
Fetching compressed AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database6.json
Fetching compressed AlphaFold Q9Y287 from
https://alphafold.ebi.ac.uk/files/AF-Q9Y287-F1-model_v6.cif
Chain information for AlphaFold Q9Y287 #1
---
Chain | Description | UniProt
A | Integral membrane protein 2B | ITM2B_HUMAN 1-266
Color AlphaFold Q9Y287 by residue attribute pLDDT_score
> ui tool show Distances
> select clear
> select /A:80
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:200
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select /A:200
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:200 @Ca
1 atom, 1 residue, 1 model selected
> select #1/A:80 @Ca
1 atom, 1 residue, 1 model selected
Exactly two atoms must be selected!
> select clear
> select #1/A:200 @Ca
1 atom, 1 residue, 1 model selected
> select #1/A:80 @Ca
1 atom, 1 residue, 1 model selected
Exactly two atoms must be selected!
> select #1/A:80@Ca
1 atom, 1 residue, 1 model selected
> select #1/A:80@Ca #1/A:200 @Ca
2 atoms, 2 residues, 1 model selected
> distance /A:80@CA /A:200@CA
Distance between /A ALA 80 CA and HIS 200 CA: 40.325Å
> close session
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/CD2CD58merge_measure.cxc" format cmd
> open CD2CD58merge.cif
Summary of feedback from opening CD2CD58merge.cif
---
warnings | Unknown polymer entity '1' on line 112
Unknown polymer entity '2' on line 1374
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for CD2CD58merge.cif #1
---
Chain | Description
A | HUMAN CD2 PROTEIN
B | HUMAN CD58 PROTEIN
> color #1 bychain
> color ~#1:1-215 #808080 transparency 70 target ac
> shape cylinder radius 1.0 fromPoint 6.92,-7.59,89.20 toPoint
> 68.86,44.41,-34.22 color yellow
> shape sphere radius 2.5 center 6.92,-7.59,89.20 color red
> shape sphere radius 2.5 center 68.86,44.41,-34.22 color red
> 2dlabels text "CD2CD58merge: 14.76 nm" xpos 0.05 ypos 0.9 color black size
> 24
> view
executed CD2CD58merge_measure.cxc
> close session
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/3GJF_HLA A*2:01_only.cif" format mmcif
No such database '/users/hwu/library/cloudstorage/box-box/jun lab group
folder/data for young-wook/harry wu/collaborations/structure prediction for
heightdb/chimerax/3gjf_hla a*2'
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/3GJF_HLA_A*201_only_measure.cxc" format cmd
> open 3GJF_HLA_A*201_only.cif
Chain information for 3GJF_HLA_A*201_only.cif #1
---
Chain | Description
D | HLA class I histocompatibility antigen, A-2 alpha chain
E | Beta-2-microglobulin
F | NYESO-1 peptide
3GJF_HLA_A*201_only.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> color #1 bychain
> color ~#1:0-276 #808080 transparency 70 target ac
> shape cylinder radius 1.0 fromPoint 39.24,8.14,34.22 toPoint
> -26.71,25.38,37.76 color yellow
> shape sphere radius 2.5 center 39.24,8.14,34.22 color red
> shape sphere radius 2.5 center -26.71,25.38,37.76 color red
> 2dlabels text "3GJF_HLA_A*201_only: 6.83 nm" xpos 0.05 ypos 0.9 color black
> size 24
> view
executed 3GJF_HLA_A*201_only_measure.cxc
> close session
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/3GJF_d6f2a_measure.cxc" format cmd
> open 3GJF_d6f2a.cif
Summary of feedback from opening 3GJF_d6f2a.cif
---
warnings | Unknown polymer entity '4' on line 4488
Missing or incorrect sequence information. Inferred polymer connectivity.
Atom H is not in the residue template for MET /A:1
Chain information for 3GJF_d6f2a.cif #1
---
Chain | Description
A | No description available
D | HLA class I histocompatibility antigen, A-2 alpha chain
E | Beta-2-microglobulin
F | NYESO-1 peptide
> color #1 bychain
> color ~#1:0-276 #808080 transparency 70 target ac
> shape cylinder radius 1.0 fromPoint 38.94,2.55,29.79 toPoint
> -52.11,43.45,48.41 color yellow
> shape sphere radius 2.5 center 38.94,2.55,29.79 color red
> shape sphere radius 2.5 center -52.11,43.45,48.41 color red
> 2dlabels text "3GJF_d6f2a: 10.15 nm" xpos 0.05 ypos 0.9 color black size 24
> view
executed 3GJF_d6f2a_measure.cxc
> close session
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/3GJF 0nvi6 d6f2a.cxs" format session
> view name session-start
opened ChimeraX session
> close session
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/3GJF_d6f2a_measure.cxc" format cmd
> open 3GJF_d6f2a.cif
Summary of feedback from opening 3GJF_d6f2a.cif
---
warnings | Unknown polymer entity '4' on line 4488
Missing or incorrect sequence information. Inferred polymer connectivity.
Atom H is not in the residue template for MET /A:1
Chain information for 3GJF_d6f2a.cif #1
---
Chain | Description
A | No description available
D | HLA class I histocompatibility antigen, A-2 alpha chain
E | Beta-2-microglobulin
F | NYESO-1 peptide
> color #1 bychain
> color ~#1:0-276 #808080 transparency 70 target ac
> shape cylinder radius 1.0 fromPoint 38.94,2.55,29.79 toPoint
> -52.11,43.45,48.41 color yellow
> shape sphere radius 2.5 center 38.94,2.55,29.79 color red
> shape sphere radius 2.5 center -52.11,43.45,48.41 color red
> 2dlabels text "3GJF_d6f2a: 10.15 nm" xpos 0.05 ypos 0.9 color black size 24
> view
executed 3GJF_d6f2a_measure.cxc
> close session
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/CD2CD58merge_measure.cxc" format cmd
> open CD2CD58merge.cif
Summary of feedback from opening CD2CD58merge.cif
---
warnings | Unknown polymer entity '1' on line 112
Unknown polymer entity '2' on line 1374
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for CD2CD58merge.cif #1
---
Chain | Description
A | HUMAN CD2 PROTEIN
B | HUMAN CD58 PROTEIN
> color #1 bychain
> color ~#1:1-215 #808080 transparency 70 target ac
> shape cylinder radius 1.0 fromPoint 6.92,-7.59,89.20 toPoint
> 68.86,44.41,-34.22 color yellow
> shape sphere radius 2.5 center 6.92,-7.59,89.20 color red
> shape sphere radius 2.5 center 68.86,44.41,-34.22 color red
> 2dlabels text "CD2CD58merge: 14.76 nm" xpos 0.05 ypos 0.9 color black size
> 24
> view
executed CD2CD58merge_measure.cxc
> select /B:186
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:182
10 atoms, 9 bonds, 1 residue, 1 model selected
> sequence chain #1/A
Alignment identifier is 1/A
> select /B:172
6 atoms, 5 bonds, 1 residue, 1 model selected
> close session
> open /Users/hwu/Desktop/HeightDB/CD2CD58merge.cif format mmcif
No such file/path: /Users/hwu/Desktop/HeightDB/CD2CD58merge.cif
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/CD2CD58merge.cxs"
> view name session-start
opened ChimeraX session
> select /B:209
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /B:209-215
58 atoms, 59 bonds, 7 residues, 1 model selected
> select clear
> select /B:209
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /B:209-215
58 atoms, 59 bonds, 7 residues, 1 model selected
> delete sel
> select clear
> save "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/CD2CD58merge.cif" relModel #5
Not saving entity_poly_seq for non-authoritative sequences
> close session
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/CD2CD58merge_measure.cxc"
> open CD2CD58merge.cif
Summary of feedback from opening CD2CD58merge.cif
---
warnings | Unknown polymer entity '1' on line 112
Unknown polymer entity '2' on line 1374
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for CD2CD58merge.cif #1
---
Chain | Description
A | HUMAN CD2 PROTEIN
B | HUMAN CD58 PROTEIN
> color #1 bychain
> color ~#1:1-208 #808080 transparency 70 target ac
> shape cylinder radius 1.0 fromPoint 6.45,-6.16,90.14 toPoint
> 62.15,36.49,-20.74 color yellow
> shape sphere radius 2.5 center 6.45,-6.16,90.14 color red
> shape sphere radius 2.5 center 62.15,36.49,-20.74 color red
> 2dlabels text "CD2CD58merge: 13.12 nm" xpos 0.05 ypos 0.9 color black size
> 24
> view
executed CD2CD58merge_measure.cxc
> close session
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/AF2/test_0d0a1/test_0d0a1_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"
Chain information for
test_0d0a1_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> color bfactor
4547 atoms, 311 residues, atom bfactor range 33.2 to 98.7
> close session
> open /Users/hwu/Downloads/ChimeraX/AlphaFold/AF-Q9Y287-F1-model_v6.cif
> format mmcif
Chain information for AF-Q9Y287-F1-model_v6.cif #1
---
Chain | Description | UniProt
A | Integral membrane protein 2B | ITM2B_HUMAN 1-266
Color AF-Q9Y287-F1-model_v6.cif by residue attribute pLDDT_score
> color bfactor
2134 atoms, 266 residues, atom bfactor range 24.6 to 98
> close session
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/AF2/test_14818 (IgG1 CAR
> ECD)/test_14818_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb"
Chain information for
test_14818_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> color bfactor
5811 atoms, 394 residues, atom bfactor range 24.4 to 98.4
> sequence chain #1/A
Alignment identifier is 1/A
> select /A:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:1-101
1478 atoms, 1491 bonds, 101 residues, 1 model selected
> select clear
> select /A:120-121
22 atoms, 21 bonds, 2 residues, 1 model selected
> select /A:118-120
41 atoms, 40 bonds, 3 residues, 1 model selected
> select /A:120-146
416 atoms, 418 bonds, 27 residues, 1 model selected
> select /A:301
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:301-388
1322 atoms, 1337 bonds, 88 residues, 1 model selected
> select clear
> select /A:248
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:248-249
24 atoms, 23 bonds, 2 residues, 1 model selected
> select /A:248-291
632 atoms, 644 bonds, 44 residues, 1 model selected
> select /A:248
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:248-285
541 atoms, 551 bonds, 38 residues, 1 model selected
> select /A:287
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:286
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /A:248-286
558 atoms, 568 bonds, 39 residues, 1 model selected
> select clear
> select /A:286
17 atoms, 16 bonds, 1 residue, 1 model selected
> delete #1A:1-286
Missing or invalid "atoms" argument: invalid atoms specifier
> delete #1/A:1-286
> select /A:394
23 atoms, 22 bonds, 1 residue, 1 model selected
> select /A:387-394
122 atoms, 122 bonds, 8 residues, 1 model selected
> select /A:385-394
146 atoms, 147 bonds, 10 residues, 1 model selected
> select /A:394
23 atoms, 22 bonds, 1 residue, 1 model selected
> select /A:388-394
108 atoms, 108 bonds, 7 residues, 1 model selected
> delete sel
> select clear
> save "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/14818_IgG1_only.cif" relModel #1
Not saving entity_poly_seq for non-authoritative sequences
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/14818_IgG1_only_measure.cxc"
> open 14818_IgG1_only.cif
Summary of feedback from opening 14818_IgG1_only.cif
---
warnings | Unknown polymer entity '1' on line 106
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for 14818_IgG1_only.cif #2
---
Chain | Description
A | No description available
> color #1 bychain
> color ~#1:287-387 #808080 transparency 70 target ac
> shape cylinder radius 1.0 fromPoint 7.35,10.76,17.68 toPoint
> -30.85,-9.09,17.28 color yellow
> shape sphere radius 2.5 center 7.35,10.76,17.68 color red
> shape sphere radius 2.5 center -30.85,-9.09,17.28 color red
> 2dlabels text "14818_IgG1_only: 4.31 nm" xpos 0.05 ypos 0.9 color black size
> 24
> view
executed 14818_IgG1_only_measure.cxc
===== 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: 1.12 (2026-06-12)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Model Number: MYD82LL/A
Chip: Apple M1
Total Number of Cores: 8 (4 Performance and 4 Efficiency)
Memory: 8 GB
System Firmware Version: 18000.120.36
OS Loader Version: 18000.120.36
Software:
System Software Overview:
System Version: macOS 26.5.1 (25F80)
Kernel Version: Darwin 25.5.0
Time since boot: 54 days, 3 hours, 56 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
accessible-pygments: 0.0.5
aiohappyeyeballs: 2.6.2
aiohttp: 3.13.4
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.13.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 26.1.0
babel: 2.18.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 4.4.3
bs4: 0.0.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.7
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.2
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.2
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: 1.67.1
ChimeraX-AtomicLibrary: 14.4
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: 1.4.1
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.4
ChimeraX-Cluster: 1.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.1
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.12
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: 1.2.2
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: 1.4.1
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: 1.8.2
ChimeraX-Label: 1.5
ChimeraX-LightingGUI: 1.0
ChimeraX-ListInfo: 1.3.1
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.3
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-MatchAlign: 1.2
ChimeraX-MatchMaker: 2.4.1
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.2.0
ChimeraX-MDcrds: 2.19
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.9
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.23
ChimeraX-ModelPanel: 1.6.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
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: 1.15.4
ChimeraX-OpenFold: 1.0
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.13
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: 1.6
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.8.2
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: 3.5.12
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.18
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-SNFG: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.3
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: 2.5.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.4
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.50.8
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.6.2
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: 8.4.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.14.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.2.4
debugpy: 1.8.21
decorator: 5.3.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.63.0
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.16.0
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.18
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 2.0.0
iniconfig: 2.3.0
ipykernel: 7.1.0
ipython: 9.9.0
ipython_pygments_lexers: 1.1.1
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.8.0
jupyter_core: 5.9.1
kiwisolver: 1.5.0
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: 0.2.2
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.1
narwhals: 2.22.1
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: 8.4.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.7
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: 4.10.0
plotly: 6.8.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.5.2
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: 2.13.4
pydantic-settings: 2.14.1
pydantic_core: 2.46.4
pydata-sphinx-theme: 0.18.0
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.5.1
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: 6.10.2
PyQt6-Qt6: 6.10.2
PyQt6-WebEngine-commercial: 6.10.0
PyQt6-WebEngine-Qt6: 6.10.2
PyQt6_sip: 13.10.3
pytest: 9.0.3
pytest-cov: 7.1.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.2
python-multipart: 0.0.32
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
rpds-py: 2026.5.1
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.1.1
sortedcontainers: 2.4.0
soupsieve: 2.8.4
Sphinx: 9.0.4
sphinx-autodoc-typehints: 3.6.1
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: 3.4.4
stack-data: 0.6.3
starlette: 1.3.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 3.2.1
threadpoolctl: 3.6.0
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.7
tqdm: 4.68.2
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
Unidecode: 1.4.0
urllib3: 2.7.0
uvicorn: 0.49.0
wcwidth: 0.8.1
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
yarl: 1.24.2
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